4dn-dcic/rpairix

R binder for pairix - 2D/1D genomic indexing and querying on bgzipped text file

rpairix's Issues

querying for multiple coordinates

take a vector of coordinates for px_query

separate line counts for individual query

wildcard query

separator as an option inside index - indexer, access function

core dump when chr name doesn't exist

If you query for '10:1-200000|20' when chromosome names are 'chr10' not '10', it produces core dump. Do a safe exit.

Codecov not run properly

@SooLee Just noticing this in successful Travis builds:

Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> package_coverage -> add_hooks -> readLines -> file
In addition: Warning messages:
1: In utils::install.packages(repos = NULL, lib = tmp_lib, pkg$path,  :
  installation of package ‘/home/travis/build/4dn-dcic/Rpairix’ had non-zero exit status
2: In file(con, "r") :
  cannot open file '/tmp/RtmpcY81mB/R_LIBS323bc6cc5bc/Rpairix/R/Rpairix': No such file or directory
Execution halted

I'll look into this at some point

bed file query

read column heading from header

Add 1d query on 2D index

Add 1D query for for 2d files

1. 10:1-2000000|*
2. *|10:1-2000000
3. --virtual4c 10:1-200000

indexer

indexer function. index on bgzipped file.
also bgzip?

seg fault when 2D query is given on 1D indexed file

px_query("samples/SRR1171591.variants.snp.vqsr.p.vcf.gz","chr10:1-20000000|chr20",6000000)

*** caught segfault ***
address 0x20, cause 'memory not mapped'

Exit smoothly.

GenomicRanges queries

increase default max mem

2000000 easily handled.