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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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added added

removed removed

src/join.h

#ifndef __JOIN_H

#define __JOIN_H

// functions to split a string by a specific delimiter

#include <string>

#include <vector>

#include <sstream>

#include <string.h>

// join a vector of elements by a delimiter object. ostream<< must be defined

// for both class S and T and an ostream, as it is e.g. in the case of strings

// and character arrays

template<class S, class T>

std::string join(std::vector<T>& elems, S& delim) {

std::stringstream ss;

typename std::vector<T>::iterator e = elems.begin();

ss << *e++;

for (; e != elems.end(); ++e) {

ss << delim << *e;

}

return ss.str();

}

// same for lists

template<class S, class T>

std::string join(std::list<T>& elems, S& delim) {

std::stringstream ss;

typename std::list<T>::iterator e = elems.begin();

ss << *e++;

for (; e != elems.end(); ++e) {

ss << delim << *e;

}

return ss.str();

}

#endif

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