lindenb/jvarkit

Java utilities for Bioinformatics

JVARKIT

Java utilities for Bioinformatics

Documentation

Documentation is available at: https://jvarkit.readthedocs.io/

Download

A pre-compiled jar is available at https://uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH .

Compilation

Since 2023, most tools (but not all) are now packaged into one application jvarkit.jar. Tools that were executed like java -jar toolname.jar are now executed as java -jar jvarkit.jar toolname. The documentation is not always up to date on this point.

See the documentation at https://jvarkit.readthedocs.io/.

Conda / Bioconda

A conda package created by DrYak is available at https://bioconda.github.io/recipes/jvarkit/README.html

Containers

jvarkit is available as a Docker container at https://hub.docker.com/r/lindenb/jvarkit . The jar is compiled under /opt/jvarkit/dist/jvarkit.jar so a command should be docker run java -jar /opt/jvarkit/dist/jvarkit.jar . Nevertheless GUI/Swing applications don't work.

Author

Pierre Lindenbaum PhD

@yokofakun

jvarkit's Issues

compilation error...?

Hi,

I am new to java, and I have a problem with compiling this tool. I see this error message when I type 'ant clean':
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

What should I do?
Thanks.

Blast2Sam error

Hi,

I am using blast2sam from jvarkit. It worked fine at first. Then I started to get an Error message

This is my command:
java -jar ../jvarkit/dist/blast2sam.jar -r reference.fa -o blast_output.sam blast_output.xml
[INFO/BlastToSam] 2016-05-23 17:57:36 "Starting JOB at Mon May 23 17:57:36 CEST 2016 com.github.lindenb.jvarkit.tools.blast2sam.BlastToSam version=265b0d11a280ad1458038fbd838a7a866952facf built=2016-04-22:11-04-17"
[INFO/BlastToSam] 2016-05-23 17:57:36 "Command Line args : -r reference.fa -o blast_output.sam blast_output.xml"
[INFO/BlastToSam] 2016-05-23 17:57:36 "Executing as [email protected] on Linux 3.19.8-100.fc20.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_77-b03"
[INFO/BlastToSam] 2016-05-23 17:57:36 "opening reference.fa"
[INFO/BlastToSam] 2016-05-23 17:57:36 "Reading from blast_output.xml"
[INFO/BlastToSam] 2016-05-23 17:57:36 "resolveEntity:-//NCBI//NCBI BlastOutput/EN/http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd/null"
[SEVERE/BlastToSam] 2016-05-23 17:57:38 "null"
java.lang.IllegalStateException
at com.github.lindenb.jvarkit.tools.blast2sam.BlastToSam.convertIterationToSequenceIteration(BlastToSam.java:288)
at com.github.lindenb.jvarkit.tools.blast2sam.BlastToSam.run_single(BlastToSam.java:239)
at com.github.lindenb.jvarkit.tools.blast2sam.BlastToSam.doWork(BlastToSam.java:739)
at com.github.lindenb.jvarkit.util.AbstractCommandLineProgram.instanceMain(AbstractCommandLineProgram.java:501)
at com.github.lindenb.jvarkit.util.AbstractCommandLineProgram.instanceMainWithExit(AbstractCommandLineProgram.java:515)
at com.github.lindenb.jvarkit.tools.blast2sam.BlastToSam.main(BlastToSam.java:761)
[INFO/BlastToSam] 2016-05-23 17:57:38 "End JOB status=-1 [Mon May 23 17:57:38 CEST 2016] com.github.lindenb.jvarkit.tools.blast2sam.BlastToSam done. Elapsed time: 0.04 minutes."
[SEVERE/BlastToSam] 2016-05-23 17:57:38 "##### ERROR: return status = -1################"

Then I reinstalled it.

java -jar jvarkit/dist/blast2sam.jar -r reference.fa -o blast_output.sam blast_output.xml
[main] INFO jvarkit - Starting JOB at Mon May 23 17:54:20 CEST 2016 com.github.lindenb.jvarkit.tools.blast2sam.BlastToSam version=ea11a24eac02ecb6ad28cadeefb035ae076e5a9d built=2016-05-23:16-05-50
[main] INFO jvarkit - Command Line args : -r reference.fa -o blast_output.sam blast_output.xml
[main] INFO jvarkit - Executing as [email protected] on Linux 3.19.8-100.fc20.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_77-b03
java.lang.RuntimeException: Option r was not defined ot dictionary missing
at com.github.lindenb.jvarkit.util.command.Command.wrapException(Command.java:262)
at com.github.lindenb.jvarkit.tools.blast2sam.BlastToSam.call(BlastToSam.java:644)
at com.github.lindenb.jvarkit.tools.blast2sam.AbstractBlastToSam.call(AbstractBlastToSam.java:494)
at com.github.lindenb.jvarkit.tools.blast2sam.AbstractBlastToSam.call(AbstractBlastToSam.java:32)
at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExceptions(Command.java:549)
at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:586)
at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExit(Command.java:592)
at com.github.lindenb.jvarkit.tools.blast2sam.BlastToSam.main(BlastToSam.java:739)
[main] ERROR jvarkit - Option r was not defined ot dictionary missing
[main] ERROR jvarkit - Command failed

it says option r is missing, but it is not. Also I have a sequence dictionary created using Picardtools and samtools faidx. They are fine. My xml output is fine too. I am using java 1.8. The blast2sam tool did work before but now it doesn't anymore. I'm not a java programmer and can't get what is wrong. I would very much appreciate some help. Many thanks!!

Nadia

MAPQ should be 0

Finally got bamstats04 to work, but at one point I get this error:

htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 9505, Read name HWI-D00104:87:D1GYYACXX:5:1112:13918:71031, MAPQ should be 0 for unmapped read.
at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:452)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:643)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:628)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:598)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:831)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:821)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:787)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:514)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:488)
at com.github.lindenb.jvarkit.tools.bamstats04.BamStats04.doWork(BamStats04.java:96)
at com.github.lindenb.jvarkit.util.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:178)
at com.github.lindenb.jvarkit.tools.bamstats04.BamStats04.main(BamStats04.java:192)

This is a samtools issue, for some reason it produces reads without MAPQ 0 when unmapped. I used bwa to align and samtools to convert to bam and sort it. Is there a way to make bamstat ignore this error?

error overlapping PCR intervals - pcrclipreads

Verify

• jdk1.8.0_72/bin/java

Subject of the issue

Describe your issue here.

Your environment

• version of jvarkit: master branch
• jdk1.8.0_72/bin/java
• the value of ${JAVA_HOME} = $HOME/java/jdk1.8.0_72
• linux centos 6.2

Even though I don't see the overlap between the two regions printed, it seems it's adding some padding (slop) between the two. See below. Any ideas?

java.lang.IllegalStateException: Overlapping PCR intervals : chr1:740716-740765 +       . chr1:740812-740861    +       .
        at com.github.lindenb.jvarkit.tools.pcr.PcrClipReads.findInterval(PcrClipReads.java:69)
        at com.github.lindenb.jvarkit.tools.pcr.PcrClipReads.findInterval(PcrClipReads.java:59)
        at com.github.lindenb.jvarkit.tools.pcr.PcrClipReads.run(PcrClipReads.java:104)
        at com.github.lindenb.jvarkit.tools.pcr.PcrClipReads.call(PcrClipReads.java:191)
        at com.github.lindenb.jvarkit.tools.pcr.AbstractPcrClipReads.call(AbstractPcrClipReads.java:450)
        at com.github.lindenb.jvarkit.tools.pcr.AbstractPcrClipReads.call(AbstractPcrClipReads.java:32)
        at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExceptions(Command.java:533)
        at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:570)
        at com.github.lindenb.jvarkit.tools.pcr.PcrClipReads.main(PcrClipReads.java:206)
[main] ERROR jvarkit - Overlapping PCR intervals : chr1:740716-740765   +       . chr1:740812-740861    +       .
[main] ERROR jvarkit - Command failed 

backlocate shifts genomic position by 1 base

I used backlocate to find the positions of the 80th and (to test) 1st amino acids of the GLA protein. From my manual calculations, the first codon for GLA is from chrX:10066889-10066891 (reverse complement) and the codon for G80 is from chrX:100658928-100658930 (reverse complement).

However, backlocate gives me the following co-ordinates:
M1: chrX:100662888-100662890 (reverse complement)
G80: chrX:100658927-100658929 (reverse complement)

I could test for more cases if you'd like it, but I have a feeling we might have some edge case calculation error for genes in the complementary strand.

blastn2snp problem

Hi
when two or more SNPs are beside each other, blastn2snp reports them in one line like this:

No definition line Homo sapiens chromosome 6, alternate assembly CHM1_1.1 1 9 21 74567818 - TAG ATC 18 A TC TAG .|.

Is it possible blastn2snp reports each snp separately ? I really need it.
Thanks

Best

SAXParseException when building backlocate

Can run all the steps under "Download & Install" on the Compilation page fine, but when I try to compile backlocate with ant backlocate, I get the following error:

Buildfile: /scratch/ukapd/jvarkit/jvarkit/build.xml

backlocate:

BUILD FAILED
/scratch/ukapd/jvarkit/jvarkit/build.xml:1854: The following error occurred while executing this line:
/scratch/ukapd/jvarkit/jvarkit/build.xml:198: The following error occurred while executing this line:
/scratch/ukapd/jvarkit/jvarkit/build.xml:8: java.util.InvalidPropertiesFormatException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
    at java.util.XMLUtils.load(XMLUtils.java:76)
    at java.util.Properties.loadFromXML(Properties.java:868)
    ....(trim)....

ant -version is Apache Ant(TM) version 1.9.2 compiled on July 8 2013

The first few lines of build.xml are:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE project SYSTEM "build.dtd">
<project name="jvarkit" default="all" basedir=".">
<property file="build.properties"/>
<property name="http.proxy" value="localhost:80"/>
<property name="generated.dir" value="src/main/generated-sources/java"/>
<property name="test.output" value="tests"/>
<property file="${htsjdk.home}/htsjdk.version.property.xml"/>

<!--define htsjdk.home if is not defined in the file "build.properties" -->
<property name="htsjdk.home" value="htsjdk"/>
...

The content of ./htsjdk/htsjdk.version.property.xml is:

#htsjdk version
#Fri, 15 Aug 2014 11:02:22 +0100

htsjdk-version=1.117

build.properties is entirely commented out

error when running the packages

Hi, I'm really new at this, and I'm probably doing something stupid but I don't have anyone to ask
I'm trying to use vcfgo and I manage to install the jvarkit with ant, after I run ant vcfgo it says build successful, but when I try to run the test of vcfgo

java -jar dist/vcfgo.jar ../snpEff/file.eff.vcf ../snpEff/file_go.vcf

I keep getting this:

Exception in thread "main" java.lang.NoClassDefFoundError: htsjdk/variant/vcf/VCFHeaderLine
at java.lang.Class.getDeclaredMethods0(Native Method)
at java.lang.Class.privateGetDeclaredMethods(Class.java:2442)
at java.lang.Class.getMethod0(Class.java:2685)
at java.lang.Class.getMethod(Class.java:1620)
at sun.launcher.LauncherHelper.getMainMethod(LauncherHelper.java:492)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:484)
Caused by: java.lang.ClassNotFoundException: htsjdk.variant.vcf.VCFHeaderLine
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
... 6 more

I tried to run other things in the jvarkit and the same error keeps appearing

I'm using the terminal in a MacBook Pro 2009 runing OS X Mavericks 10.9.5 with 8Gb RAM, The Java is the 7, and I got the ant apache installed with Homebrew.

Can you help me please?

How do I cite this?

Hello, any particular paper I could cite when using this tool? Or do I just say "used the BamStats04 package from the jvarkit tool (https://github.com/lindenb/jvarkit)"?
Thanks.

Compiling jvarkit

Hi, htsjdk compiled fine for me on my Fedora 20 system. When I try to compile jvarkit, though, I get this:

BUILD FAILED
/usr/local/genome/jvarkit/build.xml:8: java.util.InvalidPropertiesFormatException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.

Followed by a string of errors. On stack exchange, this error looks like there might be something called a BOM that is messing up compilation. I don't know anything about java, though. Can you suggest what I can do to fix this? I really need that sam4weblogo tool! It's the only thing out there that will convert my sam file to a fasta alignment format!

Thanks.

bamstats05 error: no stats produced

Hello,
I am trying to use bamstats05 to produce coverage stats, grouped by gene, for input bam and bed file but have run in to an error. Please help to resolve this.

My environment

• version of java = 1.8.0_91
• ${JAVA_HOME} = /usr/lib/jvm/java-8-oracle
• OS = Ubuntu 14.04 LTS

Steps to reproduce

My command: java -jar dist/bamstats05.jar \ BEDFILE=/Documents/wq/exons_bed/wq_intersect_exons_sorted.bed \ IN=/Documents/wq/revised_target_bams/qiagen/matched_exons_intersect/q_merged.bam

Actual behaviour

bamstats05 produces the following error:
[main] ERROR jvarkit - cannot execute command org.apache.commons.cli.MissingOptionException: Missing required option: B at org.apache.commons.cli.DefaultParser.checkRequiredOptions(DefaultParser.java:199) at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:130) at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:76) at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:60) at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExceptions(Command.java:487) at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:586) at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExit(Command.java:592) at com.github.lindenb.jvarkit.tools.bamstats04.BamStats05.main(BamStats05.java:332)

Thanks,
Setor

Biostar94573 : Need some additional Informations regarding Input/Output

Hi, sorry i know i need a lot of help but this time it should be far more easier.

After your so fast and so accurate answer of yesterday as to why i could not make and run jvarkit on windows, i switched for a mac and was able to both make and run jvarkit, and especially the tool i deeply need, biostar 94573. The only issue i have is that i am absolutely not familiar with command line applications, and so i struggle a bit with the input and the output. Even reading your example multiple times, i struggle to understand how i should type my input before i type the command to activate the tool, :

java -jar dist/biostar94573.jar

Because when i try to run this command with nothing before, the program seem to run, some text appear ending with "reading stdin" and after that i can type whenever i want, even enter or seemingly any sign or touch of the key board it continue to appear but nothing happen, it is like i cannot validate the input and tell the program that the input is over

So let's say i have a "seq.fas" or "seq.aln" file and i copied it in the jvarkit-master directory, what should be my script to convert it in vcf ? Should i just run the program with no input before, then type or paste my input and end it with a command or a sign that tells the computer that it is over ?

And the second part of my question concern the output, will i get a new "seq.vcf" file somewhere in the jvarkit-master directory or in another directory or will i have to copy the whole text starting with "##VCF 4.0" or something close to that appearing in the shell, paste it in a new text file and name the file "seq.vcf" to get my vcf file ?

Again, really sorry to bother, i fully realize how stupid or trivial this might seem to people familiar with a command line environment but this is a real concern for me and i feel so close that i truly hope this is the last !

biostar103303 tool gives same value for "exon.count_prev_and_curr" and "exon.count_curr_and_next"

Dear Pierre,

I have noticed that these 2 columns give same values with shift in one row. For e.g. "exon.count_prev_and_curr" has values- 0,12,3,4,3,11,22 and "exon.count_curr_and_next" has values- 12,3,4,3,11,22,0.

Best wishes,
Vikas

compile error "LineIteratorImpl"

Hi, I want to use sortvcfonref2
my build.property looks at follows

bigwig.dir=/commun/data/packages/bigwig

picard.version=1.92
picard.dir=/srv/gs1/software//picard-tools/picard-tools-${picard.version}
picard.jar=${picard.dir}/picard-${picard.version}.jar
sam.jar=${picard.dir}/sam-${picard.version}.jar
variant.jar=${picard.dir}/variant-${picard.version}.jar
tribble.jar=${picard.dir}/tribble-${picard.version}.jar
berkeleydb.jar=/home/him/app/je-5.0.34/lib/je-5.0.34.jar

when I try the ant sortvcfonref2 I get the following error(error truncated)

[echo] if the next javac statement fails, check that the 'build.properties' has been properly configured. See https://github.com/lindenb/jvarkit/wiki/Compilation
[javac] Compiling 1 source file to /home/hoguneim/app/jvarkit/tmp
[javac] /home/him/app/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/sortvcfonref/SortVcfOnRef2.java:13: error: cannot find symbol
[javac] import org.broad.tribble.readers.LineIterator;
[javac] ^
[javac] symbol: class LineIterator
[javac] location: package org.broad.tribble.readers
[javac] /home/him/app/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/sortvcfonref/SortVcfOnRef2.java:14: error: cannot find symbol
[javac] import org.broad.tribble.readers.LineIteratorImpl;
[javac] ^
[javac] symbol: class LineIteratorImpl
[javac] location: package org.broad.tribble.readers
[javac] /home/him/app/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/sortvcfonref/SortVcfOnRef2.java:16: error: cannot find symbol
[javac] import org.broad.tribble.readers.LineReaderUtil;
[javac] ^

Thank you

Biostar154220/CapBam memory usage

Hi Pierre,

Thanks a lot for Biostar154220, it works nicely (most of the time, hence this issue).

The problem is related to memory. I'm running my analyses on a cluster with 16-core 128Gb machines (8gb per core), I've increased the memory -Xmx16g (from the original -Xmx512m IIRC) and it still sometimes fails. The most common scenario is that it fails on contig 1 which is the largest, but in the example below, it actually fails on 17.

I'm now solving it by requesting 4-core jobs which gives me 32G of memory, but since both the sorting and the capping in biostar154220 are single threaded, this costs me more CPU hours than necessary and a CPUh usage efficiency around 25%.

Do you have any ideas on how memory usage could be improved?

[INFO/Biostar154220] 2015-08-27 10:36:53 "Alloc memory for contig 5 N=180915260*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:37:02 " Count:2384664 Elapsed: 2 minutes Last: 5:9042344 Speed: 19.740597 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:37:12 " Count:2597941 Elapsed: 2 minutes Last: 5:36424840 Speed: 19.861782 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:37:13 "Alloc memory for contig 6 N=171115067*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:37:22 " Count:2797449 Elapsed: 2 minutes Last: 6:115669821 Speed: 19.867117 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:37:27 "Alloc memory for contig 7 N=159138663*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:37:32 " Count:2992101 Elapsed: 2 minutes Last: 7:62464387 Speed: 19.83902 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:37:48 " Count:3141130 Elapsed: 2 minutes Last: 7:109067668 Speed: 18.819529 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:37:49 "Alloc memory for contig 8 N=146364022*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:37:58 " Count:3335406 Elapsed: 2 minutes Last: 8:58173107 Speed: 18.853582 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:38:00 "Alloc memory for contig 9 N=141213431*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:38:08 " Count:3534333 Elapsed: 3 minutes Last: 9:115290284 Speed: 18.908772 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:38:10 "Alloc memory for contig 10 N=135534747*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:38:18 " Count:3740221 Elapsed: 3 minutes Last: 10:126980879 Speed: 18.992739 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:38:20 "Alloc memory for contig 11 N=135006516*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:38:28 " Count:3941682 Elapsed: 3 minutes Last: 11:91988264 Speed: 19.048384 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:38:31 "Alloc memory for contig 12 N=133851895*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:38:38 " Count:4151694 Elapsed: 3 minutes Last: 12:116147402 Speed: 19.137875 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:38:42 "Alloc memory for contig 13 N=115169878*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:38:51 " Count:4351132 Elapsed: 3 minutes Last: 13:104121043 Speed: 18.967363 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:38:53 "Alloc memory for contig 14 N=107349540*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:39:02 " Count:4405922 Elapsed: 4 minutes Last: 14:71376418 Speed: 18.3357 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:39:08 "Alloc memory for contig 15 N=102531392*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:39:12 " Count:4615042 Elapsed: 4 minutes Last: 15:100038088 Speed: 18.438631 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:39:15 "Alloc memory for contig 16 N=90354753*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:39:21 "Alloc memory for contig 17 N=81195210*sizeof(int)"
[INFO/Biostar154220] 2015-08-27 10:39:22 " Count:4820694 Elapsed: 4 minutes Last: 17:65811570 Speed: 18.520117 record/millisec."
[INFO/Biostar154220] 2015-08-27 10:39:32 " Count:4910689 Elapsed: 4 minutes Last: 17:67025169 Speed: 18.164728 record/millisec."
slurmstepd: Job 5848089 exceeded memory limit (16402356 > 16384000), being killed
slurmstepd: *** JOB 5848089 CANCELLED AT 2015-08-27T10:39:35 *** on m77

Thanks.

Daniel

make: *** No rule to make target ... package-info.java', needed by 'biostar140111'. Stop.

Hi,
it seems the Makefile does not ensure that a make exits upon error so nobody realized this so far? Below is a current HEAD checkout:

$ make all
...
mkdir -p /var/tmp/portage/sci-biology/jvarkit-9999/work/jvarkit-9999/src/main/generated-sources/java
xjc -d /var/tmp/portage/sci-biology/jvarkit-9999/work/jvarkit-9999/src/main/generated-sources/java  -p gov.nih.nlm.ncbi.dbsnp  "http://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_current.xsd"
^M100 7628k    0 7628k    0     0   466k      0 --:--:--  0:00:16 --:--:--  354kparsing a schema...
^M100 7835k    0 7835k    0     0   451k      0 --:--:--  0:00:17 --:--:--  246k^M100 8033k    0 8033k    0     0   438k      0 --:--:--  0:00:18 --:--:--  200kcompiling a schema...
gov/nih/nlm/ncbi/dbsnp/Assay.java
gov/nih/nlm/ncbi/dbsnp/Assembly.java
gov/nih/nlm/ncbi/dbsnp/BaseURL.java
gov/nih/nlm/ncbi/dbsnp/Component.java
gov/nih/nlm/ncbi/dbsnp/ExchangeSet.java
gov/nih/nlm/ncbi/dbsnp/FxnSet.java
gov/nih/nlm/ncbi/dbsnp/MapLoc.java
gov/nih/nlm/ncbi/dbsnp/ObjectFactory.java
gov/nih/nlm/ncbi/dbsnp/PrimarySequence.java
gov/nih/nlm/ncbi/dbsnp/Rs.java
gov/nih/nlm/ncbi/dbsnp/RsLinkout.java
gov/nih/nlm/ncbi/dbsnp/RsStruct.java
gov/nih/nlm/ncbi/dbsnp/Ss.java
gov/nih/nlm/ncbi/dbsnp/package-info.java
mkdir -p /var/tmp/portage/sci-biology/jvarkit-9999/work/jvarkit-9999/src/main/generated-sources/java
make: *** No rule to make target '/var/tmp/portage/sci-biology/jvarkit-9999/work/jvarkit-9999/src/main/generated-sources/java/gov/nih/nlm/ncbi/dbsnp/gt/package-info.java', needed by 'biostar140111'.  Stop.
make: *** Waiting for unfinished jobs....

htslib doesn't upgrade

This doesn't upgrade htslib:

$ cd jvarkit
$ git pull origin
$ git submodule update
$ cd htsjdk
$ ant clean
$ ant
$ cd ..

Latest release on github is 1.119, but 1.117 is still the one present after running this.

Compilation segmentation fault

Subject of the issue

I'm trying to compile, and I get a segmentation fault error. I suspect that my version of xsltproc is not correct. Could I ask you for installation instructions on server where I don't have root access?

Your environment

• version of jvarkit: master
• version of java: 1.8.0_91
• the value of ${JAVA_HOME}: ""
• which OS: Linux 2.6.32-573.12.1.el6.x86_64

Steps to reproduce

git clone "https://github.com/lindenb/jvarkit.git"
cd jvarkit
make bioalcidae

Expected behaviour

Compilation will succeed.

Actual behaviour

Compilation fails with:

### COMPILING bioalcidae ######
mkdir -p /data/srlab/slowikow/src/jvarkit/_tmp-5196d09b3e9cc72f73d7bf08f0154f50bdadd475/META-INF /data/srlab/slowikow/src/jvarkit/dist
#generate java code if needed = a file with .xml exists, requires xsltproc, preprocessing file twice
if [ -e "/data/srlab/slowikow/src/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/bioalcidae/BioAlcidae.xml"   ] ; then mkdir -p /data/srlab/slowikow/src/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/tools/bioalcidae/ && xsltproc --xinclude --stringparam jarname 'bioalcidae' --stringparam githash  `cat  /data/srlab/slowikow/src/jvarkit/.git/refs/heads/master ` -o "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.bioalcidae.BioAlcidae.proc.xml" /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/commandpreproc.xsl "/data/srlab/slowikow/src/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/bioalcidae/BioAlcidae.xml" && xsltproc --xinclude --path "/data/srlab/slowikow/src/jvarkit/src/main/resources/xml" -o /data/srlab/slowikow/src/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/tools/bioalcidae/AbstractBioAlcidae.java /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/command2java.xsl "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.bioalcidae.BioAlcidae.proc.xml"  && xsltproc -o "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.bioalcidae.BioAlcidae.elixir.jsonx" /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/jsonxelixir.xsl "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.bioalcidae.BioAlcidae.proc.xml" && xsltproc -o "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.bioalcidae.BioAlcidae.elixir.json" /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/jsonx2json.xsl "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.bioalcidae.BioAlcidae.elixir.jsonx"   && mkdir -p /data/srlab/slowikow/src/jvarkit/doc/wiki && xsltproc -o "/data/srlab/slowikow/src/jvarkit/doc/wiki/BioAlcidae.md" /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/command2md.xsl "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.bioalcidae.BioAlcidae.proc.xml"   ; fi
/bin/bash: line 1:  1709 Segmentation fault      xsltproc --xinclude --stringparam jarname 'bioalcidae' --stringparam githash `cat  /data/srlab/slowikow/src/jvarkit/.git/refs/heads/master ` -o "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.bioalcidae.BioAlcidae.proc.xml" /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/commandpreproc.xsl "/data/srlab/slowikow/src/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/bioalcidae/BioAlcidae.xml"
make: *** [bioalcidae] Error 139

For vcffilterjs it fails like this:

make vcffilterjs
echo "### COMPILING vcffilterjs ######"
### COMPILING vcffilterjs ######
mkdir -p /data/srlab/slowikow/src/jvarkit/_tmp-5196d09b3e9cc72f73d7bf08f0154f50bdadd475/META-INF /data/srlab/slowikow/src/jvarkit/dist
#generate java code if needed = a file with .xml exists, requires xsltproc, preprocessing file twice
if [ -e "/data/srlab/slowikow/src/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VCFFilterJS.xml"   ] ; then mkdir -p /data/srlab/slowikow/src/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/tools/vcffilterjs/ && xsltproc --xinclude --stringparam jarname 'vcffilterjs' --stringparam githash  `cat  /data/srlab/slowikow/src/jvarkit/.git/refs/heads/master ` -o "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS.proc.xml" /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/commandpreproc.xsl "/data/srlab/slowikow/src/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VCFFilterJS.xml" && xsltproc --xinclude --path "/data/srlab/slowikow/src/jvarkit/src/main/resources/xml" -o /data/srlab/slowikow/src/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/tools/vcffilterjs/AbstractVCFFilterJS.java /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/command2java.xsl "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS.proc.xml"  && xsltproc -o "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS.elixir.jsonx" /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/jsonxelixir.xsl "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS.proc.xml" && xsltproc -o "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS.elixir.json" /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/jsonx2json.xsl "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS.elixir.jsonx"  && mkdir -p galaxy && xsltproc /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/tools2galaxy.xsl "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS.proc.xml" |  sed 's/__DOLLAR__//g' > galaxy/vcffilterjs.xml   ; fi
/bin/bash: line 1: 14841 Segmentation fault      xsltproc --xinclude --stringparam jarname 'vcffilterjs' --stringparam githash `cat  /data/srlab/slowikow/src/jvarkit/.git/refs/heads/master ` -o "/data/srlab/slowikow/src/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS.proc.xml" /data/srlab/slowikow/src/jvarkit/src/main/resources/xsl/commandpreproc.xsl "/data/srlab/slowikow/src/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VCFFilterJS.xml"
make: *** [vcffilterjs] Error 139

Verify

java -version
java version "1.8.0_91"
Java(TM) SE Runtime Environment (build 1.8.0_91-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.91-b14, mixed mode)

xsltproc --version
Using libxml 20706, libxslt 10126 and libexslt 815
xsltproc was compiled against libxml 20706, libxslt 10126 and libexslt 815
libxslt 10126 was compiled against libxml 20706
libexslt 815 was compiled against libxml 20706

biostar94573 and multiple sequence alignments

Maybe the MAFFT output doesn't give the proper format for your tool to run, but I am not getting correct looking results. Can you look at what MAFFT outputs here:
http://mafft.cbrc.jp/alignment/server/spool/_out151218093135893D4OpNAX8jGoYH7Tx2bF0C.html

It looks similar to your clustal sample output but without the conservation notation at the end of each segment. I even tried their fasta format with the hyphens for gaps but it gave the same looking output.

Error building 'mapuniprot'

Hi Pierre,

I get the error below when I try to build the mapuniprot tool. Other tools can be built.
I'm behind a proxy, which might be the problem, but I could not find the local.mk file referenced by the documentation...

Cheers,
Marc

make mapuniprot
mkdir -p /mnt/SRV017/share/data/dbs/UniProt/jvarkit/src/main/generated-sources/java
xjc -d /mnt/SRV017/share/data/dbs/UniProt/jvarkit/src/main/generated-sources/java -p org.uniprot "http://www.uniprot.org/support/docs/uniprot.xsd"
parsing a schema...

(process:3234): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
//bin/dbus-launch terminated abnormally with the following error: Autolaunch error: X11 initialization failed.

GConf Error: No D-BUS daemon running

compilation error since last git pull

Verify

• if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue
• export JAVA_HOME=/home/avilella/java/jdk1.8.0_72

Subject of the issue

/media/sf_Downloads/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/bio/bed/BedLine.java:41: error: cannot find symbol
return String.join(delimiter, this.tokens);
^
symbol: method join(CharSequence,String[])
location: class String
warning: /media/sf_Downloads/jvarkit/htsjdk-2.0.1/dist/htsjdk-2.0.1.jar(htsjdk/samtools/seekablestream/SeekableStream.class): major version 52 is newer than 51, the highest major version supported by this compiler.
It is recommended that the compiler be upgraded.
warning: /media/sf_Downloads/jvarkit/htsjdk-2.0.1/dist/htsjdk-2.0.1.jar(htsjdk/samtools/util/IterableOnceIterator.class): major version 52 is newer than 51, the highest major version supported by this compiler.
It is recommended that the compiler be upgraded.
1 error
17 warnings
make: *** [biostar178713] Error 1

Your environment

• version of jvarkit
• version of java
• the value of ${JAVA_HOME}
• which OS

Steps to reproduce

git pull ssh://[email protected]/lindenb/jvarkit.git master
make clean
make biostar178713

Expected behaviour

Successful compilation

Actual behaviour

Compilation error

VcfGO

Running from Ubunbtu 14.04, not sure what the problem is. I was hoping someone will take a look at the output and point me in the way to fixing it.

hart@hart-ubuntu:~/jvarkit$ java -jar dist/vcfgo.jar I=/home/hart/BigData/VCF/Ef1_7_29_2014Eff.vcf GO_INPUT=http://geneontology.org/gene-associations/gene_association.fb.gz GOA_INPUT=ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/FLY/gene_association.goa_fly.gz OUT=/home/hart/BigData/VCF/EffGO.vcf
[Thu Feb 12 12:07:53 CST 2015] com.github.lindenb.jvarkit.tools.vcfgo.VcfGeneOntology GOA=ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/FLY/gene_association.goa_fly.gz GO=http://geneontology.org/gene-associations/gene_association.fb.gz IN=/home/hart/BigData/VCF/Ef1_7_29_2014Eff.vcf OUT=/home/hart/BigData/VCF/EffGO.vcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Feb 12 12:07:53 CST 2015] Executing as hart@hart-ubuntu on Linux 3.13.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_75-b13; Picard version: null JdkDeflater
INFO 2015-02-12 12:07:53 AbstractVCFFilter reading from /home/hart/BigData/VCF/Ef1_7_29_2014Eff.vcf
INFO 2015-02-12 12:07:53 AbstractVCFFilter writing to /home/hart/BigData/VCF/EffGO.vcf
INFO 2015-02-12 12:07:53 AbstractVcfGeneOntology read GO http://geneontology.org/gene-associations/gene_association.fb.gz
java.io.IOException: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1]
Message: Content is not allowed in prolog.
at com.github.lindenb.jvarkit.tools.vcfgo.AbstractVcfGeneOntology.readGO(AbstractVcfGeneOntology.java:60)
at com.github.lindenb.jvarkit.tools.vcfgo.VcfGeneOntology.doWork(VcfGeneOntology.java:35)
at com.github.lindenb.jvarkit.util.vcf.AbstractVCFFilter.doWork(AbstractVCFFilter.java:73)
at com.github.lindenb.jvarkit.util.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
at com.github.lindenb.jvarkit.util.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:120)
at com.github.lindenb.jvarkit.tools.vcfgo.VcfGeneOntology.main(VcfGeneOntology.java:89)
Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1]
Message: Content is not allowed in prolog.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:598)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(XMLEventReaderImpl.java:83)
at com.github.lindenb.jvarkit.util.go.GoTree.parse(GoTree.java:286)
at com.github.lindenb.jvarkit.util.go.GoTree.parse(GoTree.java:311)
at com.github.lindenb.jvarkit.tools.vcfgo.AbstractVcfGeneOntology.readGO(AbstractVcfGeneOntology.java:55)
... 5 more
ERROR 2015-02-12 12:07:54 AbstractVCFFilter
java.io.IOException: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1]
Message: Content is not allowed in prolog.
at com.github.lindenb.jvarkit.tools.vcfgo.AbstractVcfGeneOntology.readGO(AbstractVcfGeneOntology.java:60)
at com.github.lindenb.jvarkit.tools.vcfgo.VcfGeneOntology.doWork(VcfGeneOntology.java:35)
at com.github.lindenb.jvarkit.util.vcf.AbstractVCFFilter.doWork(AbstractVCFFilter.java:73)
at com.github.lindenb.jvarkit.util.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
at com.github.lindenb.jvarkit.util.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:120)
at com.github.lindenb.jvarkit.tools.vcfgo.VcfGeneOntology.main(VcfGeneOntology.java:89)
Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1]
Message: Content is not allowed in prolog.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:598)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(XMLEventReaderImpl.java:83)
at com.github.lindenb.jvarkit.util.go.GoTree.parse(GoTree.java:286)
at com.github.lindenb.jvarkit.util.go.GoTree.parse(GoTree.java:311)
at com.github.lindenb.jvarkit.tools.vcfgo.AbstractVcfGeneOntology.readGO(AbstractVcfGeneOntology.java:55)
... 5 more
ERROR 2015-02-12 12:07:54 AbstractVCFFilter Commandline was : com.github.lindenb.jvarkit.tools.vcfgo.VcfGeneOntology GOA=ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/FLY/gene_association.goa_fly.gz GO=http://geneontology.org/gene-associations/gene_association.fb.gz IN=/home/hart/BigData/VCF/Ef1_7_29_2014Eff.vcf OUT=/home/hart/BigData/VCF/EffGO.vcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Feb 12 12:07:54 CST 2015] com.github.lindenb.jvarkit.tools.vcfgo.VcfGeneOntology done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=501743616

I hope its just some dependancy issue. May the universe shine unending blessings on you and your progeny. -Keller

biostar94573 reference sequence reading issue

Hi Pierre,

The option -c to specify the name of the sequence to be used as reference to biostar94573 is working ok. However, I still have a issue. For my reference sequence I don't have insertions and the script is reading several positions as insertions. It is creating me problems... is it possible to read all nucleotides in the reference sequence as single SNP only?

For example:
For position 8 I got as ref allele "GGT" and as alt allele "GTC". Reading in this way, I am missing variants at position 9 G/T and position 10 T/C. Furthermore, the position 8 (indeed) has no variation in my set of sequences.

Many thanks in advance,

Vanessa

Can it take input with only 2 sequecnes?

Hello, Pierre!
I'm comparing mRNA sequences between human and orangutan to find out SNP's in CDS.
I used 'MUSCLE' to generate clustal-like output and ran 'biostar94573' to obtain a vcf file, but it gave me an error.

[INFO/Biostar94573] 2015-12-22 14:21:47 "Starting JOB at Tue Dec 22 14:21:47 KST 2015 com.github.lindenb.jvarkit.tools.biostar.Biostar94573 version=undefined  built=2015-12-22:13-12-33"
[INFO/Biostar94573] 2015-12-22 14:21:47 "Command Line args : 1.seq.clw"
[INFO/Biostar94573] 2015-12-22 14:21:47 "Executing as bio1@bio1 on Linux 3.13.0-73-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_66-b17"
[INFO/Biostar94573] 2015-12-22 14:21:47 "Reading from 1.seq.clw"
[SEVERE/Biostar94573] 2015-12-22 14:21:47 "MSA format not recognized in MUSCLE (3.8) multiple sequence alignment"
[INFO/Biostar94573] 2015-12-22 14:21:47 "End JOB status=-1 [Tue Dec 22 14:21:47 KST 2015] com.github.lindenb.jvarkit.tools.biostar.Biostar94573 done. Elapsed time: 0.00 minutes."
[SEVERE/Biostar94573] 2015-12-22 14:21:47 "##### ERROR: return status = -1################"

I'm wondering if this happened because my input had only two entries.
Would it be a problem to run this tool?

My input looks like below...

MUSCLE (3.8) multiple sequence alignment


ABI1_hg         ------------------------------------------------------------
ABI1_pa         GGGAGAAATAAACGCTCGCGAGAGAACGAGGTTCAGGCGGCTGCGCGAAGTGGGTGGAGG


ABI1_hg         ------------------------------------------------------------
ABI1_pa         GGTGCCGGAGAGAGTGAGGAGGAAGGGGAGGAGGTGCAGTCCCACAATACCAGGCGGGAG


ABI1_hg         ------------------------------------------------------------
ABI1_pa         GGCGGGTAGGCGGTTCGTATCCGGGCTGTGAGGTGCTCGGAGCCTCGGCGGACCTTGCTG


ABI1_hg         ----------------------------------------------ATGGCAGAGCTGCA
ABI1_pa         CCTCTGTCTCTTTAACGCGAGAGGAAGCGATGCAGAGGGGTGGAAAATGGCAGAGCTGCA
                                                              **************

ABI1_hg         GATGTTACTAGAGGAGGAGATCCCGTCTGGCAAGAGGGCGCTGATCGAGAGTTACCAGAA
ABI1_pa         GATGTTACTAGAGGAGGAGATCCCGTCTGGCAAGAGGGCGCTGATCGAGAGTTACCAGAA
                ************************************************************

ABI1_hg         CCTGACTCGGGTGGCAGACTACTGTGAAAACAACTACATACAGGCTACAGACAAGAGAAA
ABI1_pa         CCTGACTCGGGTGGCGGACTACTGTGAAAACAACTACATACAGGCTACAGACAAGAGAAA
                *************** ********************************************

ABI1_hg         AGCTTTAGAGGAGACCAAAGCCTATACAACCCAATCTCTAGCTAGTGTTGCTTATCAAAT
ABI1_pa         AGCTTTAGAAGAGACCAAAGCCTATACAACCCAATCTCTAGCTAGTGTTGCTTATCAAAT
                ********* **************************************************

ABI1_hg         AAATGCATTGGCCAACAATGTACTCCAGTTGCTGGATATCCAAGCCTCTCAGCTTCGGAG
ABI1_pa         AAATGCATTGGCCAACAATGTACTCCAGTTGCTGGATATCCAAGCCTCTCAGCTTCGGAG
                ************************************************************

ABI1_hg         AATGGAGTCTTCCATCAATCATATCTCACAGACTGTGGATATTCATAAGGAGAAAGTGGC
ABI1_pa         AATGGAGTCTTCCATCAATCATATCTCACAGACTGTGGATATTCATAAAGAGAAAGTGGC
                ************************************************ ***********

ABI1_hg         ACGAAGAGAGATTGGTATTTTGACAACAAATAAGAATACATCAAGAACTCACAAAATAAT
ABI1_pa         TCGAAGAGAGATTGGTATTTTGACAACAAATAAGAATACATCAAGAACTCACAAAATAAT
                 ***********************************************************

ABI1_hg         AGCACCTGCGAATATGGAGCGCCCTGTAAGGTATATTCGGAAACCTATCGATTACACAGT
ABI1_pa         AGCACCTGCGAATATGGAGCGCCCTGTAAGGTATATTCGGAAACCTATCGATTACACAGT
                ************************************************************

ABI1_hg         TCTGGATGATGTGGGCCATGGTGTCAAGTGGCTAAAAGCCAAGCATGGAAATAACCAGCC
ABI1_pa         TCTGGATGATGTGGGCCATGGTGTCAAGTGGCTAAAAGCCAAGCATGGAAATAACCAGCC
                ************************************************************

ABI1_hg         TGCAAGAACTGGCACACTGTCGAGAACAAATCCTCCTACTCAGAAACCGCCAAGTCCTCC
ABI1_pa         TGCAAGAACTGGCACACTGTCGAGAACAAATCCTCCTACTCAGAAACCGCCAAGTCCTCC
                ************************************************************

ABI1_hg         CATGTCAGGCCGGGGAACACTGGGACGGAATACTCCTTATAAAACCCTGGAACCTGTTAA
ABI1_pa         CATGTCAGGCCGGGGAACACTGGGACGGAATACTCCTTATAAAACCCTGGAACCTGTTAA
                ************************************************************

ABI1_hg         ACCCCCAACAGTTCCTAATGACTATATGACCAGTCCTGCTAGGCTTGGAAGTCAGCATAG
ABI1_pa         ACCCCCAACAGTTCCTAATGACTATATGACCAGTCCTGCTAGGCTTGGAAGTCAGCATAG
                ************************************************************

ABI1_hg         TCCAGGCAGGACAGCATCTTTAAATCAGAGACCAAGGACACACAGTGGAAGTAGTGGAGG
ABI1_pa         TCCAGGCAGGACAGCATCTTTAAATCAGAGACCAAGGACACACAGTGGAAGTAGTGGAGG
                ************************************************************

multipass PcrClipReads

Verify

• master branch or varkit

Subject of the issue

I would like to know how to best do a multipass PcrClipReads on the sam bam file

Expected behaviour

I would like to start with a bam file and a collection of bed files to run through in order.
For reads falling outside the bed file, print out the bam entries as is.
For reads falling inside the bed file, clip and print out.
Once done for the first bam file, repeat the process with the second bed file.
Each intermediate bam files should be exactly the same as the initial bam file, only with more clipping or fully discarded reads at every pass.

Actual behaviour

I believe the current default options for PcrClipReads only prints out the reads affected, but does not print any of the unaffected reads. Maybe simply needs an extra --print_all option?

MIN_COVERAGE doesn't seem to work

java version "1.8.0_91" - Ubuntu 14.04

MIN_COVERAGE doesn't seem to work

When I give a BAM file as input along with a BED file with my regions of interest and choose MIN_COVERAGE as 5, I still get results with min of 0.

Error making vcfrenamesamples

Hi,

We're getting errors making vcfrenamesamples on our cluster. Full make stack below:

maa@pcs5a:/nfs/pathogen004/maa/jvarkit$ make vcfrenamesamples
mkdir -p /nfs/pathogen004/maa/jvarkit/
rm -rf /nfs/pathogen004/maa/jvarkit/1.128.zip /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/ 
echo "Downloading HTSJDK 1.128 with curl"
Downloading HTSJDK 1.128 with curl
curl  -x "webcache.sanger.ac.uk:3128" -o /nfs/pathogen004/maa/jvarkit/1.128.zip -L "https://github.com/samtools/htsjdk/archive/1.128.zip"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   119    0   119    0     0    316      0 --:--:-- --:--:-- --:--:--   318
100 9326k    0 9326k    0     0  4031k      0 --:--:--  0:00:02 --:--:-- 9206k
unzip /nfs/pathogen004/maa/jvarkit/1.128.zip -d /nfs/pathogen004/maa/jvarkit/
Archive:  /nfs/pathogen004/maa/jvarkit/1.128.zip
429f2a8585d9c98a3efd4cedc5188b60b1e66ac5
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/.classpath  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/.gitignore  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/.project  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/.travis.yml  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/README.md  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/etc/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/etc/test/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/etc/test/junit-noframes.xsl  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/etc/test/testng.css  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/examplestore  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/htsjdk.iml  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/htsjdk.ipr  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/commons-jexl-2.1.1.jar  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/commons-logging-1.1.1.jar  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/jni/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/jni/libIntelDeflater.so  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/snappy-java-1.0.3-rc3.jar  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/testng/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/testng/testng-5.5-jdk15.jar  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/pom.xml  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/c/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/c/inteldeflater/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/c/inteldeflater/IntelDeflater.c  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/AbstractBAMFileIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/AbstractSAMHeaderRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/AlignmentBlock.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/AsyncSAMFileWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMFileConstants.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMFileReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMFileWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMIndexContent.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMIndexMetaData.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMIndexWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMIndexer.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMRecordCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BamFileIoUtils.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BamIndexValidator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/Bin.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinList.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinaryBAMIndexWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinaryCigarCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinaryTagCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinningIndexBuilder.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinningIndexContent.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BrowseableBAMIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CRAMFileReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CRAMFileWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CRAMIndexer.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CRAMIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CachingBAMFileIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/Chunk.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/Cigar.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CigarElement.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CigarOperator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/ComparableSamRecordIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CustomReaderFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/DefaultSAMRecordFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/Defaults.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/DiskBasedBAMFileIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/DuplicateScoringStrategy.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/FileTruncatedException.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/FixBAMFile.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/GenomicIndexUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/LinearIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/MergingSamRecordIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/NotPrimarySkippingIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/QueryInterval.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/ReservedTagConstants.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMBinaryTagAndValue.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMException.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileHeader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileSource.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileSpan.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileTruncatedReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileWriterFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileWriterImpl.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFormatException.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMHeaderRecordComparator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMLineParser.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMProgramRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMReadGroupRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordComparator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordCoordinateComparator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordQueryNameComparator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordSetBuilder.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMSequenceDictionary.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMSequenceRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMSortOrderChecker.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTag.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTagUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTestUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTextHeaderCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTextReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTextWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTools.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMUtils.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMValidationError.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SQTagUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamFileHeaderMerger.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamFileValidator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamFiles.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamInputResource.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamPairUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamReaderFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamStreams.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/StreamInflatingIndexingOutputStream.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/TagValueAndUnsignedArrayFlag.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/TextCigarCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/TextTagCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/TextualBAMIndexWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/ValidationStringency.java  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/apps/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/apps/TimeChannel.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/apps/TimeRandomAccessFile.java  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/ContainerFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/ContainerParser.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/Cram2SamRecordFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/CramBuilder.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/CramIO.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/CramNormalizer.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/Sam2CramRecordFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/Utils.java  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/CramVersions.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/IntHashMap.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/MutableInt.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/NonforgivingPrintStream.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/NullOutputStream.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/Version.java  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/encoding/
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 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/compressed.sam.gz  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/coordinate_sorted.sam  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/empty.bai  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/empty.bam  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/empty_no_empty_gzip_block.bai  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/empty_no_empty_gzip_block.bam  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/intervallist/
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  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestCompInverseManual.interval_list  
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  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManualComp.interval_list  
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  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/io/5newline5.txt  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/io/empty.txt  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/io/slurptest.txt  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/issue76.bam  
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/liftover/
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/reference/
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  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.noindex.fasta  
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/util/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/util/QualityEncodingDetectorTest/
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 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/util/QualityEncodingDetectorTest/illumina-as-standard.bam  
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 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/util/defective_bgzf.bam  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/util/no_bgzf_terminator.bam  
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/tribble/tmp/
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/variant/utils/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/variant/utils/SamSequenceDictionaryExtractor/
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C1.1/
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C10.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C11.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C12.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C13.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C14.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C15.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C16.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C17.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C18.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C19.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C2.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C20.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C21.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C22.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C23.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C24.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C25.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C26.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C27.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C28.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C29.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C3.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C30.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C31.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C32.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C33.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C34.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C35.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C36.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C37.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C38.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C39.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C4.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C40.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C41.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C42.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C43.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C44.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C45.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C46.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C47.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C48.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C49.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C5.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C50.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C51.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C52.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C53.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C54.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C55.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C56.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C57.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C58.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C59.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C6.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C60.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C61.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C62.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C63.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C64.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C65.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C66.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C7.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C8.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C9.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/s_1_1101.filter  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/L001/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/L001/s_1_1101.clocs  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C10.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C11.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C12.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C13.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C14.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C15.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C16.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C17.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C18.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C19.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C2.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C20.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C21.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C22.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C23.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C24.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C25.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/N.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/tribble/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/tribble/tmp/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/tribble/tmp/.gitignore  
find /nfs/pathogen004/maa/jvarkit/htsjdk-1.128 -exec touch '{}'  ';'
rm -f /nfs/pathogen004/maa/jvarkit/1.128.zip
echo "Compiling htsjdk with ${JAVA_HOME} = /software/pathogen/external/apps/usr/local/jdk1.7.0_21/"
Compiling htsjdk with /software/pathogen/external/apps/usr/local/jdk1.7.0_21/ = /software/pathogen/external/apps/usr/local/jdk1.7.0_21/
echo "Compiling htsjdk library for java. Requires  apache ANT. If it fails here, it's a not a problem with jvarkit."
Compiling htsjdk library for java. Requires  apache ANT. If it fails here, it's a not a problem with jvarkit.
(cd /nfs/pathogen004/maa/jvarkit/htsjdk-1.128 && ant )
Buildfile: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml

write-version-property:
[propertyfile] Creating new property file: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/htsjdk.version.properties

init:

compile-samtools:
    [mkdir] Created dir: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/classes
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:244: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 371 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/io/ByteBufferUtils.java:360: warning: CRC16 is internal proprietary API and may be removed in a future release
    [javac]         sun.misc.CRC16 crc16 = new sun.misc.CRC16();
    [javac]                 ^
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/io/ByteBufferUtils.java:360: warning: CRC16 is internal proprietary API and may be removed in a future release
    [javac]         sun.misc.CRC16 crc16 = new sun.misc.CRC16();
    [javac]                                            ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 3 warnings

compile-tribble:
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:244: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 72 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-variant:
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:244: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 61 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] Note: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/variant/vcf/AbstractVCFCodec.java uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-src:

compile-samtools-tests:
    [mkdir] Created dir: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testclasses
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:265: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 67 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testclasses
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-tribble-tests:
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:265: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 23 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testclasses
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-variant-tests:
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:265: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 20 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testclasses
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] Note: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/tests/java/htsjdk/variant/variantcontext/GenotypeLikelihoodsUnitTest.java uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-tests:

compile:

htsjdk-jar:
    [mkdir] Created dir: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist
      [jar] Building jar: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/htsjdk-1.128.jar
     [copy] Copying 3 files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist

all:

BUILD SUCCESSFUL
Total time: 25 seconds
touch --no-create /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/commons-jexl-2.1.1.jar
mkdir -p /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/
echo "package com.github.lindenb.jvarkit.util.htsjdk;" > /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo '@javax.annotation.Generated("jvarkit")' >> /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public class HtsjdkVersion{ private HtsjdkVersion(){}' >> /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getVersion() {return "1.128";}' >> /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getHome() {return "/nfs/pathogen004/maa/jvarkit/htsjdk-1.128";}' >> /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo '}'  >> /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo "### COMPILING vcfrenamesamples ######"
### COMPILING vcfrenamesamples ######
mkdir -p /nfs/pathogen004/maa/jvarkit/_tmp-1.128/META-INF /nfs/pathogen004/maa/jvarkit/dist-1.128 galaxy-bundle/jvarkit
#create galaxy
rm -f galaxy-bundle/vcfrenamesamples.xml
xsltproc --path /nfs/pathogen004/maa/jvarkit/src/main/resources/xml --output galaxy-bundle/jvarkit/vcfrenamesamples.xml --stringparam name "vcfrenamesamples" --stringparam class "com.github.lindenb.jvarkit.tools.misc.VcfRenameSamples" --stringparam classpath "commons-jexl-2.1.1.jar commons-logging-1.1.1.jar htsjdk-1.128.jar snappy-java-1.0.3-rc3.jar vcfrenamesamples.jar" --stringparam version  `cat  /nfs/pathogen004/maa/jvarkit/.git/refs/heads/master ` /nfs/pathogen004/maa/jvarkit/src/main/resources/xsl/tools2galaxy.xsl /nfs/pathogen004/maa/jvarkit/src/main/resources/xml/tools.xml || echo "XSLT failed (ignored)"
XSLT failed (ignored)
cp galaxy-bundle/jvarkit/vcfrenamesamples.xml /nfs/pathogen004/maa/jvarkit/_tmp-1.128/META-INF/galaxy.xml 
cp: cannot stat `galaxy-bundle/jvarkit/vcfrenamesamples.xml': No such file or directory
make: [vcfrenamesamples] Error 1 (ignored)
#copy resource
cp /nfs/pathogen004/maa/jvarkit/src/main/resources/messages/messages.properties /nfs/pathogen004/maa/jvarkit/_tmp-1.128
#compile
javac -d /nfs/pathogen004/maa/jvarkit/_tmp-1.128 -g -classpath "/nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/commons-jexl-2.1.1.jar:/nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/commons-logging-1.1.1.jar:/nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/htsjdk-1.128.jar:/nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/snappy-java-1.0.3-rc3.jar" -sourcepath /nfs/pathogen004/maa/jvarkit/src/main/java:/nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java /nfs/pathogen004/maa/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfRenameSamples.java
/nfs/pathogen004/maa/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:268: illegal start of type
        LinkedHashSet<String> vcfFiles= new LinkedHashSet<>(inputs.size()+1);
                                                          ^
/nfs/pathogen004/maa/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:171: cannot find symbol
symbol  : constructor GZIPOutputStream(java.io.FileOutputStream,boolean)
location: class java.util.zip.GZIPOutputStream
            return new GZIPOutputStream(new FileOutputStream(file),true);
                   ^
2 errors
make: *** [vcfrenamesamples] Error 1

Curl issue in Makefile when downloading htsjdk

Hi Pierre,

While using jvarkit for the first time, I ran into an issue when compiling sam2tsv and wanted to let others know the solution in case they encountered a similar issue.

I kept getting an error with curl and ca certificates when trying to compile sam2tsv

$ make sam2tsv

mkdir -p /home4/user/software/jvarkit/
rm -rf /home4/user/software/jvarkit/2.0.1.zip /home4/user/software/jvarkit/htsjdk-2.0.1/
echo "Downloading HTSJDK 2.0.1 with curl"
Downloading HTSJDK 2.0.1 with curl
curl -o /home4/user/software/jvarkit/2.0.1.zip -L "https://github.com/samtools/htsjdk/archive/2.0.1.zip"
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0curl: (77) error setting certificate verify locations:
CAfile: /etc/pki/tls/certs/ca-bundle.crt
CApath: none
make: *** [home4/user/software/jvarkit/htsjdk-2.0.1/build.xml] Error 77

I went and looked Makefile and found that by adding the -k option (allows insecure transfers), everything worked great. Every other time curl was in used Makefile it had the -k option.

line 589: curl -k ${curl.proxy} -o $(dir ${htsjdk.home})${htsjdk.version}.zip -L "https://github.com/samtools/htsjdk/archive/${htsjdk.version}.zip"

sam validation error from pcrclipreads

Verify

• if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue
• the version of java

Subject of the issue

NS500125:197:H7LJJAFXX:3:11406:4401:11023_1:N:0:GCCAAT:TTACCT, 
Soft clipping CIGAR operator can only be inside of hard clipping operator

Your environment

• version of jvarkit: master branch
• version of java: jdk1.8.0_72
• the value of ${JAVA_HOME}: $HOME/java/jdk1.8.0_72
• which OS

Steps to reproduce

I ran PcrClipReads followed by samtools view and samtools sort. I then ran Picard alignment summary and got the error above for one of the reads.

Expected behaviour

No issues

Actual behaviour

Got SAM validation error. The full line of the read in question is below:

NS500125:197:H7LJJAFXX:3:11406:4401:11023_1:N:0:GCCAAT:TTACCT   0       chr8    95836647        23      92M1S1D51S      *       0       0       ATAGTAGTTGTTTAAAGTAAGTTAGAGAAATGTAGTAATAGTAATGTTTATTTATGTGGTTGGTTATTTTTTTTTGTAATGTAAAGAAATAATTAAGAAATGGAGTTAGGGTTTTTATAGTTGTTTTGAGAAATTTTGAAGATA EE<A/A<E/A/EAEEAAEEEA<AAAAAEAEAA6AAAEAAAA<EAEEEEEEEEEAAAAAA/AA6AEEAEEAEEEEEEAEEEEEEEEEEEE6EEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEE        MD:Z:1C2C7C4C4C12C2C2C4C0C0C2C11C0C5C0C4C16^TAA0C11C6C0C1C1C2C2C11C6C1  XG:Z:CT NM:i:30 XM:Z:.x..x.......h....h....x............h..x..h....hhh..h...........hh.....hh....h................h...........h......hh.h.x..x..h...........x......h.    XR:Z:GA

would like a VCF sample renamer

be able to rename samples using either

• a simple lookup table

oldname1 newname1
oldname2 newname2

• an argument list whose length matched the number of samples in the vcf

java -jar dist/renamesamples.jar newname1 newname2 (stdin|file1.vcf) > file2.vcf

backlocate errors out

Hi,

I installed jvarkit and backlocate as described in the documentation. I also placed mysql-connector-java-5.1.31-bin.jar in a custom location and added the mysql.jar variable in build.properties to point to it. However, when I run echo -e "GLA\tA143P" | java -jar dist/backlocate.jar, I get the following error:

[INFO/BackLocate] 2014-09-11 09:55:34 "Starting JOB at Thu Sep 11 09:55:34 EDT 2014 com.github.lindenb.jvarkit.tools.backlocate.BackLocate version=796ed1daa01c438fe99027105e17588a82e764f0  built=2014-07-10 12:25:05"
[INFO/BackLocate] 2014-09-11 09:55:34 "Command Line args : (EMPTY/NO-ARGS)"
[INFO/BackLocate] 2014-09-11 09:55:34 "Executing as [email protected] on Mac OS X 10.9.4 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_65-b14-466.1-11M4716"
[SEVERE/BackLocate] 2014-09-11 09:55:34 "com.mysql.jdbc.Driver"
java.lang.ClassNotFoundException: com.mysql.jdbc.Driver
    at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:171)
    at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.doWork(BackLocate.java:557)
    at com.github.lindenb.jvarkit.util.AbstractCommandLineProgram.instanceMain(AbstractCommandLineProgram.java:456)
    at com.github.lindenb.jvarkit.util.AbstractCommandLineProgram.instanceMainWithExit(AbstractCommandLineProgram.java:470)
    at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.main(BackLocate.java:634)
[SEVERE/BackLocate] 2014-09-11 09:55:34 "cannot.load.mysql.driver"
Exception in thread "main" java.lang.NoClassDefFoundError: htsjdk/samtools/util/CloserUtil
    at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.doWork(BackLocate.java:629)
    at com.github.lindenb.jvarkit.util.AbstractCommandLineProgram.instanceMain(AbstractCommandLineProgram.java:456)
    at com.github.lindenb.jvarkit.util.AbstractCommandLineProgram.instanceMainWithExit(AbstractCommandLineProgram.java:470)
    at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.main(BackLocate.java:634)
Caused by: java.lang.ClassNotFoundException: htsjdk.samtools.util.CloserUtil
    at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
    ... 4 more

How would I address this please? Thank you!

SamToPsl adds the flag to the bed name field

this is not documented and I don't see where it makes sense to do this.

FixVcfMissingGenotypes can't find bams

Hi! Thanks for writing this awesome tool, it's exactly what I need. I'm having some issues running it though. Specifically, I get a warning:

[WARNING/FixVcfMissingGenotypes] 2015-11-25 18:08:30 "No bam to fix sample M-Ait9.22003_GTCTGTCA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam"

I created a 2 sample vcf by merging 2 vcfs:

vcf-merge M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.mpileup.all.snp.vcfsamp.vcf.vcf.gz M-Ait9.22003_GTCTGTCA_C5E9DANXX_6_20140930B_20140930.bam.mpileup.all.snp.vcfsamp.vcf.vcf.gz > Ait14-Ait9.vcf

Then I made a bam list:

find ./ -name "M-Ait*" > bams.txt

And I reheadered the vcf file to make sure the sample names match:

bcftools reheader -s bams.txt Ait14.Ait9.vcf > reheadered.vcf

Then I run FixVcfMissingGenotypes:

java -jar ~/Documents/Science/software/jvarkit/dist-1.139/fixvcfmissinggenotypes.jar -d 10 -f bams.txt reheadered.vcf > fixed.vcf

But I get the following error:

[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:22 "Starting JOB at Wed Nov 25 18:08:22 CET 2015 com.github.lindenb.jvarkit.tools.misc.FixVcfMissingGenotypes version=1518314284a5c8c26ae674daeb32ec3badf3b79c  built=2015-11-24:15-11-48"
[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:22 "Command Line args : -d 10 -f bams.txt reheadered.vcf"
[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:22 "Executing as [email protected] on Mac OS X 10.9.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15"
[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:23 "Reading header for M-Ait9.22003_GTCTGTCA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam"
[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:24 "Reading header for M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam"
Nov 25, 2015 6:08:25 PM com.github.lindenb.jvarkit.util.vcf.VCFUtils createVcfIterator
INFO: reading from reheadered.vcf
[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:25 "Adding 'java.io.tmpdir' directory to the list of tmp directories"
[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:25 "Sample: M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam"
[WARNING/FixVcfMissingGenotypes] 2015-11-25 18:08:25 "No bam to fix sample M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam"
[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:30 "done sample M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam fixed=0 not-fixed=0 total=495705 genotypes"
Nov 25, 2015 6:08:30 PM com.github.lindenb.jvarkit.util.vcf.VCFUtils createVcfIteratorFromFile
INFO: reading vcf from /var/folders/xv/172vhqrn0t3d_6w0by980t8r0000gn/T/fixvcf8957134055780526493.vcf
[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:30 "Sample: M-Ait9.22003_GTCTGTCA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam"
[WARNING/FixVcfMissingGenotypes] 2015-11-25 18:08:30 "No bam to fix sample M-Ait9.22003_GTCTGTCA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam"
[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:32 "done sample M-Ait9.22003_GTCTGTCA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam fixed=0 not-fixed=0 total=495705 genotypes"
Nov 25, 2015 6:08:32 PM com.github.lindenb.jvarkit.util.vcf.VCFUtils createVcfIteratorFromFile
INFO: reading vcf from /var/folders/xv/172vhqrn0t3d_6w0by980t8r0000gn/T/fixvcf3450591832525368561.vcf
[INFO/FixVcfMissingGenotypes] 2015-11-25 18:08:37 "End JOB status=0 [Wed Nov 25 18:08:37 CET 2015] com.github.lindenb.jvarkit.tools.misc.FixVcfMissingGenotypes done. Elapsed time: 0.25 minutes."

The bam files definitely exist (and are in the current directory):

ls -lh
total 10896016
-rw-r--r--  1 arundurvasula  staff    22M Nov 25 17:40 Ait14-Ait9.vcf
-rw-r--r--  1 arundurvasula  staff   3.2G Nov 24 16:23 M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam
-rw-r--r--  1 arundurvasula  staff   1.9G Nov 24 16:24 M-Ait9.22003_GTCTGTCA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam
-rw-r--r--  1 arundurvasula  staff   173B Nov 25 18:08 bams.txt
-rw-r--r--  1 arundurvasula  staff   177B Nov 25 18:03 bams.txt~
-rw-r--r--  1 arundurvasula  staff    22M Nov 25 18:08 fixed.vcf
-rw-r--r--  1 arundurvasula  staff    22M Nov 25 17:46 refs.removed.vcf
-rw-r--r--  1 arundurvasula  staff    22M Nov 25 18:08 reheadered.vcf

But it looks like none of the genotypes were fixed. Any ideas? I noticed that the error gets called here: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/FixVcfMissingGenotypes.java#L207
after a call from .isEmpty(). Perhaps it isn't reading in the bam files for some reason?

Thanks again for writing this tool!

Trouble with ant when installing jvarkit

I remember I was able to bypass this somehow in the past, but nothing seems to work now.

I am trying to compile jvarkit:

@BioPower2 ~/programs/jvarkit/htsjdk $ ls /home/adrian/.ant/lib
ant-nodeps-1.7.1.jar
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 15:23:13
@BioPower2 ~/programs/jvarkit/htsjdk $ ant -lib /home/adrian/.ant/lib/
Buildfile: build.xml

write-version-property:

BUILD FAILED
/home/adrian/programs/jvarkit/htsjdk/build.xml:68: Problem: failed to create task or type propertyfile
Cause: the class org.apache.tools.ant.taskdefs.optional.PropertyFile was not found.
This looks like one of Ant's optional components.
Action: Check that the appropriate optional JAR exists in
-/usr/share/ant/lib
-/home/adrian/.ant/lib
-a directory added on the command line with the -lib argument

Do not panic, this is a common problem.
The commonest cause is a missing JAR.

This is not a bug; it is a configuration problem

Total time: 0 seconds

It doesn't seem to matter how I point to that file, it just doesn't seem to want to take it. Even if I -lib /home/adrian/.ant/lib/ant-nodeps-1.7.1.jar

Apache Ant version 1.7.1 compiled on August 24 2010

I am running CentOS 6.

Anyone have any ideas? I even tried a more recent package of ant from apache, 1.9.4, but there is no nodeps file for it and there is still error.

Issues making Jvarkit

Here it s,
i REALLY REALLY need to use Biostar 94573 to convert some FASTA files into VCF so i will try again cause i have no other choices (even top Bioinformatics software like Artemis or Geneious cannot accept FASTA as an input and produce VCF as an output). I succesfully installed make, and successfully "made" curl.

When i run the first command line of your example:

$ curl https://raw.githubusercontent.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln

(Actually in the example you provide in "https://github.com/lindenb/jvarkit/wiki/Biostar94573"
the adress is
https://raw.github.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln
and i had to change it to https://raw.githubusercontent.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln
but that's just a detail !)

I get the same output as you :
CLUSTAL W (1.81) multiple sequence alignment

gi|6273285|gb|AF191659.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273284|gb|AF191658.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273287|gb|AF191661.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273286|gb|AF191660.1|AF191 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273290|gb|AF191664.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273289|gb|AF191663.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273291|gb|AF191665.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
******* **** *************************************

gi|6273285|gb|AF191659.1|AF191 TATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATA
gi|6273284|gb|AF191658.1|AF191 TATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATA
gi|6273287|gb|AF191661.1|AF191 TATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATA
gi|6273286|gb|AF191660.1|AF191 TATATA----------ATATATTTATAATTTCCTTATATATCCAAATATA
gi|6273290|gb|AF191664.1|AF191 TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA
gi|6273289|gb|AF191663.1|AF191 TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA
gi|6273291|gb|AF191665.1|AF191 TATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATA
****** ******** **** ********* *********

gi|6273285|gb|AF191659.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGT
gi|6273284|gb|AF191658.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273287|gb|AF191661.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273286|gb|AF191660.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273290|gb|AF191664.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273289|gb|AF191663.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTAT
gi|6273291|gb|AF191665.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
************************************ *********** *

gi|6273285|gb|AF191659.1|AF191 ACCAGA
gi|6273284|gb|AF191658.1|AF191 ACCAGA
gi|6273287|gb|AF191661.1|AF191 ACCAGA
gi|6273286|gb|AF191660.1|AF191 ACCAGA
gi|6273290|gb|AF191664.1|AF191 ACCAGA
gi|6273289|gb|AF191663.1|AF191 ACCAGA
gi|6273291|gb|AF191665.1|AF191 ACCAGA
******
But when i try to make any tool, i still got an error message saying :

makefile:167: multiple target patterns. Stop.

I made sure i had Java 1.7, when i run "java -version" i get :

Java version "1.7.0_51"
Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
Java HotSpot(TM) Client VM (build 24.51-b03, mixed mode, sharing)

I also added every single possible required folder to my PATH to make
sure i had all the requisite folders in it. Here is my PATH :

C:\ProgramFiles\OpenVPN\bin;C:;C:\mingw\msys\1.0\bin;C:\mingw\msys\1.0\lib;C:\mingw\bin;C:\mingw\lib;C:\Perl\bin;C:\Perl\lib;C:\Perl;C:\mingw\msys;C:\mingw;C:\curl-7.43.0;C:\Program Files\Git\bin;C:\Program Files\Git\lib;C:\Program Files\Git;C:\Program Files\Java\jdk.1.7.0_79;C:\Program Files\Java\jdk.1.7.0_79\bin;C:\Program Files\Java\jdk.1.7.0_79\Git\bin;C:\Program Files\Java\jdk.1.7.0_79\Git;C:\Program Files\Java\jdk.1.7.0_79\apache-ant-1.9.5;C:\Program Files\Java\jdk.1.7.0_79\Git;C:\Program Files\Java\jdk.1.7.0_79/bin;C:\Program Files\Java\jdk.1.7.0_79\Git;C:\Program Files\Java\jre7;C:\Program Files\Java\jre7/bin;C:\Program Files\Java\jre7/lib;

and finally, googling my error i was told by two different websites to check for colons
in target names so i copied and pasted the makefile in word and searched for colons
but word did not found a single one. I re downloaded jvarkit using the git clone command :

$ git clone "https://github.com/lindenb/jvarkit.git"

a few days ago so i guess i have the latest version of javrkit.

Please, could you try to help me ?

Genotyping of all positions

Hi Pierre,

Thanks for this! Would it be possible to output EVERY position on the reference as VCF format? (no coverage = ./., and if same as reference = 0/0)? Otherwise I can't merge VCF files of different samples together....

ability to copy particular fields in vcfviewgui

I'm not sure how easy it is to implement but it would be handy to be able to copy particular fields. As it is now, the whole row that is selected is copied.

BamStats04 does not recognize IN= or I=

Hello,
This is a bit odd:

@BioPower3-IBM ~/Rozella/mapping $ ll
total 17G
drwxrwxr-x. 2 adrian adrian 4.0K Mar 26 15:15 .
drwxrwxr-x. 6 adrian adrian 4.0K Mar 26 12:33 ..
-rw-rw-r--. 1 adrian adrian 0 Mar 26 15:18 Contig_coverage.table
-rw-rw-r--. 1 adrian adrian 23K Mar 26 14:39 Contig_ranges2.bed
-rw-rw-r--. 1 adrian adrian 25K Mar 26 14:34 Contigs.stats
-rw-rw-r--. 1 adrian adrian 6.5G Mar 26 13:39 Rozella.bam
-rw-rw-r--. 1 adrian adrian 5.1G Mar 26 14:16 Rozella.sort.bam
-rw-rw-r--. 1 adrian adrian 5.1G Mar 26 14:57 Rozella.sort.grp.bam
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 15:22:35
@BioPower3-IBM ~/Rozella/mapping $ ~/programs/jvarkit/dist-1.128/bamstats04 IN=Rozella.sort.grp.bam BED=Contig_ranges2.bed VALIDATION_STRINGENCY=LENIENT > Contig_coverage.table
ERROR: Option 'IN' is required.
...
@BioPower3-IBM ~/Rozella/mapping $ ~/programs/jvarkit/dist-1.128/bamstats04 IN=Rozella.sort.grp.bam BED=Contig_ranges2.bed
ERROR: Option 'IN' is required.
...
@BioPower3-IBM ~/Rozella/mapping $ ~/programs/jvarkit/dist-1.128/bamstats04 IN="Rozella.sort.grp.bam" BED=Contig_ranges2.bed VALIDATION_STRINGENCY=LENIENT > Contig_coverage.table
ERROR: Option 'IN' is required.
...
@BioPower3-IBM ~/Rozella/mapping $ ~/programs/jvarkit/dist-1.128/bamstats04 I=Rozella.sort.grp.bam BED=Contig_ranges2.bed VALIDATION_STRINGENCY=LENIENT > Contig_coverage.table
ERROR: Option 'IN' is required.
...

Any idea what could be going on? I tried other BAM files too, same issue.
Adrian

boum ### vs ### error when running blastn2snp

[~]>java -jar /usr/local/jvarkit/dist/blastn2snp.jar < /main/data/tmp/infilem7.out |column -t
[main] INFO jvarkit - Starting JOB at Tue May 03 16:16:59 PDT 2016 com.github.lindenb.jvarkit.tools.blast.BlastNToSnp version=undefined built=2016-05-03:11-05-55
[main] INFO jvarkit - Command Line args : (EMPTY/NO-ARGS)
[main] INFO jvarkit - Executing as hhough@compute2 on Linux 3.2.0-89-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_77-b03
[main] INFO jvarkit - Reading from stdin
[main] INFO jvarkit - resolveEntity:-//NCBI//NCBI BlastOutput/EN/http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd/null
java.lang.IllegalStateException: boum 406 vs 1
at com.github.lindenb.jvarkit.tools.blast.BlastNToSnp.run(BlastNToSnp.java:282)
at com.github.lindenb.jvarkit.tools.blast.BlastNToSnp.call(BlastNToSnp.java:338)
at com.github.lindenb.jvarkit.tools.blast.AbstractBlastNToSnp.call(AbstractBlastNToSnp.java:274)
at com.github.lindenb.jvarkit.tools.blast.AbstractBlastNToSnp.call(AbstractBlastNToSnp.java:32)
at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExceptions(Command.java:549)
at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:586)
at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExit(Command.java:592)
at com.github.lindenb.jvarkit.tools.blast.BlastNToSnp.main(BlastNToSnp.java:357)

query hit hit-index hsp-index query-POS hit-POS STRAND REF(hit) ALT(query) blast.align_length blast.hit.var blast.query.var blast.mid. var

[main] ERROR jvarkit - boum 406 vs 1
scaffold_1:46694924 Pp01 1 1 304 43120910 + C Y 203 C Y .
[main] ERROR jvarkit - Command failed

java version "1.8.0_77"
$JAVA_HOME : /usr/local/java
Ubuntu 12.04

I'm unsure why the boum error is being thrown. We've tried to use different input files and the result is the same, though the values for boum and vs differ. Is something missing that is causing this?

Avg coverage calculation

Hello,
thanks for the great tool...this is more of a question rather than an issue. I am using bamstat04 and everything works perfectly. I want to ensure that I am reading the calculations correctly and was therefore wondering if you could explain briefly how the avg coverage is calculated? Is this as follows: given 'N' reads of length 'L' mapping to a region of length 'R' with 100% of the region is covered the avg cov = N*L/R? or do you consider the coverage at each position? Thanks

compile error

Are there other dependencies other than what is listed at https://github.com/lindenb/jvarkit/wiki/Compilation?
I have this configuration file
`

bigwig.dir=/commun/data/packages/bigwig

picard.version=1.108
picard.dir=/Users/george/picard-tools-${picard.version}
picard.jar=${picard.dir}/picard-${picard.version}.jar
sam.jar=${picard.dir}/sam-${picard.version}.jar
variant.jar=${picard.dir}/variant-${picard.version}.jar
tribble.jar=${picard.dir}/tribble-${picard.version}.jar

berkeleydb.jar=/commun/data/packages/je-4.0.34/lib/je-5.0.34.jar

`
On compiling,

ant biostar92368

I get this compile error. I have truncated the error list.

biostar92368: [echo] if the next javac statement fails, check that the 'build.properties' has been properly configured. See https://github.com/lindenb/jvarkit/wiki/Compilation [javac] Compiling 1 source file to /Users/george/Softwares/jvarkit/tmp [javac] /Users/george/Softwares/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar92368.java:13: error: package org.broad.tribble.readers does not exist [javac] import org.broad.tribble.readers.LineIterator; [javac] ^ [javac] /Users/george/Softwares/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar92368.java:15: error: package net.sf.picard does not exist [javac] import net.sf.picard.PicardException; [javac] ^ [javac] /Users/george/Softwares/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar92368.java:16: error: package net.sf.samtools.util does not exist [javac] import net.sf.samtools.util.CloserUtil; [javac] ^ [javac] /Users/george/Softwares/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar92368.java:20: error: package com.sleepycat.bind.tuple does not exist [javac] import com.sleepycat.bind.tuple.StringBinding;

backlocate doesn't find some known 3' mutations

backlocate appears to have problems locating the following mutation:
echo -e "HSD3B2\tP341L" | java -jar dist/backlocate.jar -R hg19.fa
It is mutation .0011 here: http://www.omim.org/entry/613890

Alberts-MacBook-Pro:jvarkit bertgold$ echo -e "HSD3B2\tP341L" | java -jar dist/backlocate.jar -R hg19.fa
Nov 24, 2015 7:41:01 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Starting JOB at Tue Nov 24 07:41:01 CST 2015 com.github.lindenb.jvarkit.tools.backlocate.BackLocate version=undefined built=2015-11-21:07-11-51
Nov 24, 2015 7:41:01 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Command Line args : -R hg19.fa
Nov 24, 2015 7:41:01 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Executing as [email protected] on Mac OS X 10.8.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15
Nov 24, 2015 7:41:02 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
INFO: loading genes
Nov 24, 2015 7:41:04 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_ctg5_hap1
Nov 24, 2015 7:41:04 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_gl000204_random
Nov 24, 2015 7:41:04 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_gl000205_random
Nov 24, 2015 7:41:05 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr19_gl000209_random
Nov 24, 2015 7:41:05 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr1_gl000191_random
Nov 24, 2015 7:41:05 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr1_gl000192_random
Nov 24, 2015 7:41:06 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_ctg9_hap1
Nov 24, 2015 7:41:06 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_gl000193_random
Nov 24, 2015 7:41:06 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_gl000194_random
Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_apd_hap1
Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_cox_hap2
Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_dbb_hap3
Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_mann_hap4
Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_mcf_hap5
Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_qbl_hap6
Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_ssto_hap7
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr7_gl000195_random
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr9_gl000201_random
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000211
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000212
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000213
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000214
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000218
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000219
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000220
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000221
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000222
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000223
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000227
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000228
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000229
Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000237
Nov 24, 2015 7:41:09 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000241
Nov 24, 2015 7:41:09 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000243
Nov 24, 2015 7:41:09 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000247
Nov 24, 2015 7:41:09 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
INFO: genes:78827
Nov 24, 2015 7:41:09 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadkgXRefFromUri
INFO: loading http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz
Nov 24, 2015 7:41:12 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadkgXRefFromUri
INFO: kgxref:28453

User.Gene AA1 petide.pos.1 AA2 knownGene.name knownGene.strand knownGene.AA index0.in.rna wild.codon potential.var.codons base.in.rna chromosome index0.in.genomic exon

Nov 24, 2015 7:41:12 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate call
INFO: reading from stdin
Nov 24, 2015 7:41:12 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate backLocate
INFO: fetch genome
java.lang.RuntimeException: #index out of range for :uc001ehu.3 petide length=223
at com.github.lindenb.jvarkit.util.command.Command.wrapException(Command.java:252)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.backLocate(BackLocate.java:240)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.run(BackLocate.java:383)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:531)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:59)
at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:546)
at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExit(Command.java:584)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.main(BackLocate.java:566)
java.lang.IndexOutOfBoundsException: Index: 1020, Size: 669
at java.util.ArrayList.rangeCheck(ArrayList.java:635)
at java.util.ArrayList.get(ArrayList.java:411)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate$RNASequence.charAt(BackLocate.java:98)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate$ProteinCharSequence.charAt(BackLocate.java:121)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.backLocate(BackLocate.java:243)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.run(BackLocate.java:383)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:531)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:59)
at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:546)
at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExit(Command.java:584)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.main(BackLocate.java:566)
Nov 24, 2015 7:41:12 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
SEVERE: java.lang.IndexOutOfBoundsException: Index: 1020, Size: 669
Nov 24, 2015 7:41:12 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
SEVERE: Command failed

core dumped xsltproc vcffilterjs when make

hi， when running this step 'make vcffilterjs', i meet the following error and have no idea how to solve it ,could someone give me some help ? thank you very much!
(core dumped) xsltproc --xinclude -o "/datd/wangrui/bin/jvarkit/src/main/generated-sources/com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS.proc.xml" /datd/wangrui/bin/jvarkit/src/main/resources/xsl/commandpreproc.xsl "/datd/wangrui/bin/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VCFFilterJS.xml
Makefile:383: recipe for target 'vcffilterjs' failed
make: *** [vcffilterjs] Error 139

Feature request Biostar77288 - different visualisation possible ?

Hi,

thanks for the nice tools.

I wonder if it would be easy to implement a different visualisation for this tool. At the moment it is a 3D cylinder shape, yet in my view a 2D shape (i.e. similar to the ncbiblast visualisation bars) would be more effective at data display.

For example, with indel rich data (eg pacbio before quiver) the 3d ends really overexaggerate the 1bp tiny indels even when looking at long alignments, and thereby obscure other data.

Thanks,
Colin

fixvcfmissinggenotypes stuck at reading vcf from stream

Subject of the issue

I have already compile successfully for fixvcfmissinggenotypes, i think^^. And I try to run it on my linux cluster, but I found it is stuck in reading vcf from stream for two days. But I can not figure out by myself.

Your environment

• version of jvarkit

It is recent release version, directly download from github

• version of java

/apps/free/java-jdk/1.8.0_20/bin/java

• the value of ${JAVA_HOME}

/apps/free/java-jdk/1.8.0_20/bin/java

• which OS

Linux version 2.6.32-431.el6.x86_64

Steps to reproduce

$ java -jar /work/student/yafei-mao/jvarkit/dist-2.0.1/fixvcfmissinggenotypes.jar -d 20 -f bam_missing.txt test.vcf>test_2_new.vcf
[main] INFO jvarkit - Starting JOB at Thu Mar 10 09:11:40 JST 2016 com.github.lindenb.jvarkit.tools.misc.FixVcfMissingGenotypes version=2b998754ad124603692f68473c4559d8235c3c1c built=2016-03-09:09-03-28
[main] INFO jvarkit - Command Line args : -d 20 -f bam_missing.txt test.vcf
[main] INFO jvarkit - Executing as yafei-mao@sango10513 on Linux 2.6.32-431.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_73-b02
[main] INFO jvarkit - Reading header for test.vcf
DEBUG 2016-03-10 09:11:40 SRAAccession Checking if SRA module is supported in that environment
[main] INFO jvarkit - Reading header for bam_missing.txt
Mar 10, 2016 9:11:43 AM com.github.lindenb.jvarkit.util.vcf.VCFUtils createVcfIteratorFromStream
INFO: reading vcf from stream

Could you give some idea to help me figure out?
Thanks a lot~

Yafei

PreCompiled binaries?

Any chance you can precompile this for a few OS systems? Getting ant to work is a pain. I know I spend a day getting it right on one machine but forgot what was the fix and now have to do it again.

biostart94573.jar appears to hang (S+ state)

We have recently installed jvarkit, specifically to utilize biostart94573 to convert files.

However, in our case the program appears to hang, remaining in the S+ state.

We just wanted to check whether this program does indeed require a good deal of time and memory, or if there is likely something wrong with our installation/implementation, or further if we are using this tool incorrectly.

Our system in a 12 core, 200GB RAM, CENTOS 6.0 Linux system.

Example:

[root@dev01]$ /quarantine/BioStar/java_1.7/jdk1.7.0_79/bin/java -jar /quarantine/BioStar/build/jvarkit/dist-1.133/biostar94573.jar euro_samples_fasta_clustalw.aln [INFO/Biostar94573] 2015-07-14 16:45:47 "Starting JOB at Tue Jul 14 16:45:47 EDT 2015 com.github.lindenb.jvarkit.tools.biostar.Biostar94573 version=ee95fe6971b5655c61d7feb22e8fa877201a9ca6 built=2015-07-06:11-07-10"
[INFO/Biostar94573] 2015-07-14 16:45:47 "Command Line args : euro_samples_fasta_clustalw.aln"
[INFO/Biostar94573] 2015-07-14 16:45:47 "Executing as root@dev01 on Linux 2.6.32-504.12.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15"
[INFO/Biostar94573] 2015-07-14 16:45:47 "Reading from euro_samples_fasta_clustalw.aln"
[INFO/Biostar94573] 2015-07-14 16:45:47 "format : Clustal"

feature request: PcrClipReads based on a flag

Hi Pierre,

This is a feature request for the very useful pcrclipreads module. How would you envision being able to run it on a bed file, but only for reads that have a certain flag?

I am thinking an extra flag that if it's present and has a certain value, it means the read is flagged to be clipped according to the regions defined in the bed file.

Thx

DpnII site

Subject of the issue

Could you please add the DpnII site? Apart from the lack of that enzyme, everything works great.
Thank you

vcfcutsamples randomly orders samples

When a user specifies the samples to be kept vcfcutsamples should use the sample order given on the command line or in the file.

When a user specifies the inverse (omit certain samples), the existing order of samples in the original vcf should be maintained.