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Viewing changes to src/vcfgenotypes.cpp

Committer: Package Import Robot
Author(s): Andreas Tille
Date: 2016-09-16 15:52:29 UTC
Revision ID: package-import@ubuntu.com-20160916155229-24mxrntfylvsshsg

Tags: upstream-1.0.0~rc1+dfsg

Import upstream version 1.0.0~rc1+dfsg

files added:

.gitignore

.gitmodules

.travis.yml

1KG_Index

1KG_Index/1KG_IDs.txt

1KG_Index/1kG_ethnic_index.py

1KG_Index/README

LICENSE

Makefile

Makefile.old

README.md

bin/plotBfst.R

bin/plotHapLrt.R

bin/plotHaplotypes.R

bin/plotPfst.R

bin/plotSmoothed.R

bin/plotWCfst.R

bin/plotXPEHH.R

examples

examples/612.bFst_SatApr12_12_29_17.png

examples/612.counts_FriApr11_13_16_42.png

examples/612.nocounts.smoothed_TueApr15_13_25_53.png

examples/612.nocounts_FriApr11_13_16_38.png

examples/612.wcfst.txt_FriApr11_13_17_02.png

examples/example-ehh.png

examples/headCrest.haps.txt_ThuMay29_15_08_53.pdf

examples/headCrest.haps.txt_ThuMay29_15_08_53.png

examples/phasing-diff-res.png

examples/phasing-results.png

examples/scaffold612.d-stat.10kb.txt_abba-baba_WedOct29_10_17_10.png

examples/t.hapass.txt_TueJun24_11_52_08.png

examples/xp-phased.txt

examples/xp-phased.txt_TueApr29_13_20_47.png

examples/xp-unphased.txt

examples/xp-unphased.txt_TueApr29_13_20_58.png

examples/xpehh_WedApr23_11_30_10.png

fastahack

filevercmp

fsom

intervaltree

logos

logos/websiteLogo.pdf

logos/websiteLogo.png

multichoose

samples

samples/sample.vcf

samples/scaffold612.phased.vcf

samples/scaffold612.vcf

smithwaterman

src/BedReader.h

src/LD.cpp

src/Variant.cpp

src/Variant.h

src/abba-baba.cpp

src/bFst.cpp

src/cdflib.cpp

src/cdflib.hpp

src/convert.h

src/dumpContigsFromHeader.cpp

src/genotypeSummary.cpp

src/gl-XPEHH.cpp

src/gpatInfo.hpp

src/hapLrt.cpp

src/iHS.cpp

src/join.h

src/meltEHH.cpp

src/mt19937ar.h

src/normalize-iHS.cpp

src/pFst.cpp

src/pdflib.cpp

src/pdflib.hpp

src/permuteGPAT++.cpp

src/permuteGPATsmoother.cpp

src/permuteRegions.cpp

src/permuteSmooth.cpp

src/plotHaps.cpp

src/popStats.cpp

src/rnglib.cpp

src/rnglib.hpp

src/segmentFst.cpp

src/segmentIhs.cpp

src/sequenceDiversity.cpp

src/smoother.cpp

src/split.cpp

src/split.h

src/splitUniqStarts.cpp

src/ssw.c

src/ssw.h

src/ssw_cpp.cpp

src/ssw_cpp.h

src/var.cpp

src/var.hpp

src/vcf2dag.cpp

src/vcf2fasta.cpp

src/vcf2tsv.cpp

src/vcfToHap.cpp

src/vcfaddinfo.cpp

src/vcfafpath.cpp

src/vcfallelicprimitives.cpp

src/vcfaltcount.cpp

src/vcfannotate.cpp

src/vcfannotategenotypes.cpp

src/vcfbreakmulti.cpp

src/vcfcat.cpp

src/vcfcheck.cpp

src/vcfclassify.cpp

src/vcfcleancomplex.cpp

src/vcfcombine.cpp

src/vcfcommonsamples.cpp

src/vcfcountalleles.cpp

src/vcfcreatemulti.cpp

src/vcfdistance.cpp

src/vcfecho.cpp

src/vcfentropy.cpp

src/vcfevenregions.cpp

src/vcffilter.cpp

src/vcffixup.cpp

src/vcfflatten.cpp

src/vcfgeno2alleles.cpp

src/vcfgeno2haplo.cpp

src/vcfgenosamplenames.cpp

src/vcfgenosummarize.cpp

src/vcfgenotypecompare.cpp

src/vcfgenotypes.cpp

src/vcfglbound.cpp

src/vcfglxgt.cpp

src/vcfhetcount.cpp

src/vcfhethomratio.cpp

src/vcfindex.cpp

src/vcfinfo2qual.cpp

src/vcfinfosummarize.cpp

src/vcfintersect.cpp

src/vcfkeepgeno.cpp

src/vcfkeepinfo.cpp

src/vcfkeepsamples.cpp

src/vcfleftalign.cpp

src/vcflength.cpp

src/vcfnumalt.cpp

src/vcfoverlay.cpp

src/vcfparsealts.cpp

src/vcfprimers.cpp

src/vcfqual2info.cpp

src/vcfrandom.cpp

src/vcfrandomsample.cpp

src/vcfremap.cpp

src/vcfremoveaberrantgenotypes.cpp

src/vcfremovesamples.cpp

src/vcfroc.cpp

src/vcfsample2info.cpp

src/vcfsamplediff.cpp

src/vcfsamplenames.cpp

src/vcfsamplestats.cpp

src/vcfsitesummarize.cpp

src/vcfsom.cpp

src/vcfstats.cpp

src/vcfstreamsort.cpp

src/vcfuniq.cpp

src/vcfuniqalleles.cpp

src/wcFst.cpp

src/xpEHH.cpp

tabixpp

tests

tests/lib

tests/lib/Local

tests/lib/Local/vcflib

tests/lib/Local/vcflib/Test.pm

tests/vcfdistance.t

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src/vcfgenotypes.cpp

#include "Variant.h"

#include "split.h"

#include <string>

#include <iostream>

using namespace std;

using namespace vcflib;

int main(int argc, char** argv) {

if (argc != 2) {

cerr << "usage: " << argv[0] << " <vcf file>" << endl

<< "report the genotypes for each sample, for each variant in the vcf file" << endl;

return 1;

}

string filename = argv[1];

VariantCallFile variantFile;

if (filename == "-") {

variantFile.open(std::cin);

} else {

variantFile.open(filename);

}

if (!variantFile.is_open()) {

return 1;

}

Variant var(variantFile);

while (variantFile.getNextVariant(var)) {

map<string, map<string, vector<string> > >::iterator s = var.samples.begin();

map<string, map<string, vector<string> > >::iterator sEnd = var.samples.end();

cout << var.sequenceName << "\t"

<< var.position << "\t"

<< var.ref << "\t";

var.printAlt(cout); cout << "\t";

var.printAlleles(cout); cout << "\t";

for (; s != sEnd; ++s) {

map<string, vector<string> >& sample = s->second;

string& genotype = sample["GT"].front(); // XXX assumes we can only have one GT value

vector<string> gt = split(genotype, "|/");

// report the sample and it's genotype

cout << s->first << ":";

for (vector<string>::iterator g = gt.begin(); g != gt.end(); ++g) {

if (g->c_str() == ".") {

cout << ".";

} else {

int index = atoi(g->c_str());

cout << var.alleles[index];

}

if (g != (gt.end()-1)) cout << "/";

}

cout << "\t";

}

cout << endl;

}

return 0;

}

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