biowu/variationtoolkit

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variationtoolkit's Issues

Variation toolkit compilation error

I am trying to compile the variation toolkit and I am facing some problem with 
the compilation. Please find below the compiling log.

g++ -o ../bin/scanvcf scanvcf.cpp -O3 -Wall -lz
g++ -o ../bin/verticalize verticalize.cpp -O3 -Wall -lz
g++ -o ../bin/groupbygene groupbygene.cpp -O3 -Wall -lz
g++ -o ../bin/numericsplit numericsplit.cpp -O3 -Wall -lz
g++ -o ../bin/extractinfo extractinfo.cpp -O3 -Wall -lz
g++ -o ../bin/extractformat extractformat.cpp -O3 -Wall -lz
g++ -o ../bin/normalizechrom normalizechrom.cpp -O3 -Wall -lz
g++ -o ../bin/manhattan manhattan.cpp -O3 -Wall -lz
g++ -c -o xtabix.o xtabix.cpp -O3 -Wall -I 
/home/sivasubramani/Programs/tabix-0.2.6
g++ -o ../bin/vcftabix vcftabix.cpp -O3 -Wall xtabix.o  -L 
/home/sivasubramani/Programs/tabix-0.2.6  `mysql_config --cflags  --libs` -lz 
-ltabix
g++ -c -o knowngene.o knowngene.cpp -O3 -Wall
g++ -c -o xfaidx.o xfaidx.cpp -O3 -Wall -I /home/sivasubramani/Programs/samtools
g++ -c -o geneticcode.o geneticcode.cpp -O3 -Wall
g++ -o ../bin/prediction prediction.cpp -O3 -Wall knowngene.o xfaidx.o 
geneticcode.o  -L /home/sivasubramani/Programs/samtools  `mysql_config --cflags 
 --libs` -lz -lbam
g++ -o ../bin/samplespersnp samplespersnp.cpp -O3 -Wall -lz
g++ -o ../bin/dnacontext dnacontext.cpp -O3 -Wall xfaidx.o  -L 
/home/sivasubramani/Programs/samtools -lz -lbam
g++ -o ../bin/ranges ranges.cpp -O3 -Wall -lz
g++ -c -o ttview.o ttview.cpp -O3 -Wall -I /home/sivasubramani/Programs/samtools
g++ -c -o xbam.o xbam.cpp -O3 -Wall -I /home/sivasubramani/Programs/samtools 
g++ -o ../bin/vcfttview vcfttview.cpp -O3 -Wall ttview.o xbam.o xfaidx.o \
        /home/sivasubramani/Programs/samtools/bam_color.o \
        /home/sivasubramani/Programs/samtools/bam2bcf.o \
        /home/sivasubramani/Programs/samtools/errmod.o \
        -L /home/sivasubramani/Programs/samtools -L /home/sivasubramani/Programs/samtools/bcftools  -lz -lbam -lbcf
/home/sivasubramani/Programs/samtools/libbam.a(bgzf.o): In function `bgzf_mt':
/home/sivasubramani/Programs/samtools/bgzf.c:445: undefined reference to 
`pthread_create'
/home/sivasubramani/Programs/samtools/libbam.a(bgzf.o): In function 
`mt_destroy':
/home/sivasubramani/Programs/samtools/bgzf.c:458: undefined reference to 
`pthread_join'
collect2: error: ld returned 1 exit status
make[1]: *** [../bin/vcfttview] Error 1
make[1]: Leaving directory `/home/sivasubramani/Programs/variationtoolkit/src'
make: *** [all] Error 2


Best,
Siva

Original issue reported on code.google.com by [email protected] on 23 Jul 2014 at 8:40

rPsort macro in loess passes parameters to std::partial_sort in wrong order

What steps will reproduce the problem?
1. Run loess.cpp standalone with data.txt given in comments (on Mac OS X)
2.
3.

What is the expected output? What do you see instead?
Expected output:
1   1.5 1.5
3   2   2
6   7   7
9   8   8
12  15  8

Instead I get a memory fault.

What version of the product are you using? On what operating system?
Latest source on Mac OS X

Please provide any additional information below.
The rPsort macro gives parameters to std::partial_sort in wrong order, should 
be: first, middle, last.

Currently:
#define rPsort(x,n,k) std::partial_sort(&x[0],&x[n],&x[k]);

Fix:
#define rPsort(x,n,k) std::partial_sort(&x[0],&x[k],&x[n]);

Original issue reported on code.google.com by [email protected] on 2 Mar 2015 at 4:23