1 files changed, 137 insertions, 86 deletions
diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist
index 4aa9ba414bd3..20c3eeca8d4e 100644
--- a/biology/vcflib/pkg-plist
+++ b/biology/vcflib/pkg-plist
@@ -1,5 +1,7 @@
 bin/abba-baba
 bin/bFst
+bin/bed2region
+bin/bgziptabix
 bin/dumpContigsFromHeader
 bin/genotypeSummary
 bin/hapLrt
@@ -16,22 +18,29 @@ bin/segmentFst
 bin/segmentIhs
 bin/sequenceDiversity
 bin/smoother
+bin/vcf2bed.py
 bin/vcf2dag
 bin/vcf2fasta
+bin/vcf2sqlite.py
 bin/vcf2tsv
+bin/vcf_strip_extra_headers
 bin/vcfaddinfo
 bin/vcfafpath
 bin/vcfallelicprimitives
 bin/vcfaltcount
 bin/vcfannotate
 bin/vcfannotategenotypes
+bin/vcfbiallelic
 bin/vcfbreakmulti
 bin/vcfcat
 bin/vcfcheck
 bin/vcfclassify
 bin/vcfcleancomplex
+bin/vcfclearid
+bin/vcfclearinfo
 bin/vcfcombine
 bin/vcfcommonsamples
+bin/vcfcomplex
 bin/vcfcountalleles
 bin/vcfcreatemulti
 bin/vcfdistance
@@ -39,6 +48,7 @@ bin/vcfecho
 bin/vcfentropy
 bin/vcfevenregions
 bin/vcffilter
+bin/vcffirstheader
 bin/vcffixup
 bin/vcfflatten
 bin/vcfgeno2alleles
@@ -49,37 +59,65 @@ bin/vcfgenotypecompare
 bin/vcfgenotypes
 bin/vcfglbound
 bin/vcfglxgt
+bin/vcfgtcompare.sh
 bin/vcfhetcount
 bin/vcfhethomratio
+bin/vcfindelproximity
+bin/vcfindels
 bin/vcfindex
 bin/vcfinfo2qual
 bin/vcfinfosummarize
 bin/vcfintersect
+bin/vcfjoincalls
 bin/vcfkeepgeno
 bin/vcfkeepinfo
 bin/vcfkeepsamples
 bin/vcfld
 bin/vcfleftalign
 bin/vcflength
+bin/vcfmultiallelic
+bin/vcfmultiway
+bin/vcfmultiwayscripts
+bin/vcfnobiallelicsnps
+bin/vcfnoindels
+bin/vcfnosnps
+bin/vcfnulldotslashdot
+bin/vcfnullgenofields
 bin/vcfnumalt
 bin/vcfoverlay
 bin/vcfparsealts
+bin/vcfplotaltdiscrepancy.r
+bin/vcfplotaltdiscrepancy.sh
+bin/vcfplotsitediscrepancy.r
+bin/vcfplottstv.sh
 bin/vcfprimers
+bin/vcfprintaltdiscrepancy.r
+bin/vcfprintaltdiscrepancy.sh
 bin/vcfqual2info
+bin/vcfqualfilter
 bin/vcfrandom
 bin/vcfrandomsample
+bin/vcfregionreduce
+bin/vcfregionreduce_and_cut
+bin/vcfregionreduce_pipe
+bin/vcfregionreduce_uncompressed
 bin/vcfremap
 bin/vcfremoveaberrantgenotypes
+bin/vcfremovenonATGC
 bin/vcfremovesamples
 bin/vcfroc
 bin/vcfsample2info
 bin/vcfsamplediff
 bin/vcfsamplenames
 bin/vcfsitesummarize
+bin/vcfsnps
+bin/vcfsort
 bin/vcfstats
 bin/vcfstreamsort
 bin/vcfuniq
 bin/vcfuniqalleles
+bin/vcfvarstats
+bin/vcfwave
 bin/wcFst
 include/BandedSmithWaterman.h
 include/BedReader.h
@@ -88,111 +126,124 @@ include/IndelAllele.h
 include/IntervalTree.h
 include/LargeFileSupport.h
 include/LeftAlign.h
+include/LeftAlign.hpp
 include/Mosaik.h
 include/Region.h
 include/Repeats.h
 include/SmithWatermanGotoh.h
 include/Variant.h
+include/allele.hpp
 include/catch.hpp
 include/cdflib.hpp
+include/cigar.hpp
 include/convert.h
 include/disorder.h
 include/filevercmp.h
 include/gpatInfo.hpp
 include/join.h
+include/makeUnique.h
 include/mt19937ar.h
 include/multichoose.h
 include/multipermute.h
+include/murmur3.hpp
 include/pdflib.hpp
+include/rkmh.hpp
 include/rnglib.hpp
 include/split.h
 include/ssw.hpp
 include/ssw_cpp.hpp
 include/var.hpp
-include/vec128int.h
-include/veclib_types.h
+include/vcf-c-api.h
+include/vcf-wfa.h
 lib/libvcflib.a
-man/man1/man/abba-baba.1.gz
-man/man1/man/bFst.1.gz
-man/man1/man/dumpContigsFromHeader.1.gz
-man/man1/man/genotypeSummary.1.gz
-man/man1/man/hapLrt.1.gz
-man/man1/man/iHS.1.gz
-man/man1/man/meltEHH.1.gz
-man/man1/man/normalize-iHS.1.gz
-man/man1/man/pFst.1.gz
-man/man1/man/pVst.1.gz
-man/man1/man/permuteGPAT++.1.gz
-man/man1/man/permuteSmooth.1.gz
-man/man1/man/plotHaps.1.gz
-man/man1/man/popStats.1.gz
-man/man1/man/segmentFst.1.gz
-man/man1/man/segmentIhs.1.gz
-man/man1/man/sequenceDiversity.1.gz
-man/man1/man/smoother.1.gz
-man/man1/man/vcf2dag.1.gz
-man/man1/man/vcf2fasta.1.gz
-man/man1/man/vcf2tsv.1.gz
-man/man1/man/vcfaddinfo.1.gz
-man/man1/man/vcfafpath.1.gz
-man/man1/man/vcfallelicprimitives.1.gz
-man/man1/man/vcfaltcount.1.gz
-man/man1/man/vcfannotate.1.gz
-man/man1/man/vcfannotategenotypes.1.gz
-man/man1/man/vcfbreakmulti.1.gz
-man/man1/man/vcfcat.1.gz
-man/man1/man/vcfcheck.1.gz
-man/man1/man/vcfclassify.1.gz
-man/man1/man/vcfcleancomplex.1.gz
-man/man1/man/vcfcombine.1.gz
-man/man1/man/vcfcommonsamples.1.gz
-man/man1/man/vcfcountalleles.1.gz
-man/man1/man/vcfcreatemulti.1.gz
-man/man1/man/vcfdistance.1.gz
-man/man1/man/vcfecho.1.gz
-man/man1/man/vcfentropy.1.gz
-man/man1/man/vcfevenregions.1.gz
-man/man1/man/vcffilter.1.gz
-man/man1/man/vcffixup.1.gz
-man/man1/man/vcfflatten.1.gz
-man/man1/man/vcfgeno2alleles.1.gz
-man/man1/man/vcfgeno2haplo.1.gz
-man/man1/man/vcfgenosamplenames.1.gz
-man/man1/man/vcfgenosummarize.1.gz
-man/man1/man/vcfgenotypecompare.1.gz
-man/man1/man/vcfgenotypes.1.gz
-man/man1/man/vcfglbound.1.gz
-man/man1/man/vcfglxgt.1.gz
-man/man1/man/vcfhetcount.1.gz
-man/man1/man/vcfhethomratio.1.gz
-man/man1/man/vcfindex.1.gz
-man/man1/man/vcfinfo2qual.1.gz
-man/man1/man/vcfinfosummarize.1.gz
-man/man1/man/vcfintersect.1.gz
-man/man1/man/vcfkeepgeno.1.gz
-man/man1/man/vcfkeepinfo.1.gz
-man/man1/man/vcfkeepsamples.1.gz
-man/man1/man/vcfld.1.gz
-man/man1/man/vcfleftalign.1.gz
-man/man1/man/vcflength.1.gz
-man/man1/man/vcflib.1.gz
-man/man1/man/vcfnumalt.1.gz
-man/man1/man/vcfoverlay.1.gz
-man/man1/man/vcfparsealts.1.gz
-man/man1/man/vcfprimers.1.gz
-man/man1/man/vcfqual2info.1.gz
-man/man1/man/vcfrandom.1.gz
-man/man1/man/vcfrandomsample.1.gz
-man/man1/man/vcfremap.1.gz
-man/man1/man/vcfremoveaberrantgenotypes.1.gz
-man/man1/man/vcfremovesamples.1.gz
-man/man1/man/vcfroc.1.gz
-man/man1/man/vcfsample2info.1.gz
-man/man1/man/vcfsamplediff.1.gz
-man/man1/man/vcfsamplenames.1.gz
-man/man1/man/vcfsitesummarize.1.gz
-man/man1/man/vcfstats.1.gz
-man/man1/man/vcfstreamsort.1.gz
-man/man1/man/vcfuniq.1.gz
-man/man1/man/vcfuniqalleles.1.gz
-man/man1/man/wcFst.1.gz
+%%ZIG%%lib/libzig.a
+lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so
+share/man/man1/abba-baba.1.gz
+share/man/man1/bFst.1.gz
+share/man/man1/dumpContigsFromHeader.1.gz
+share/man/man1/genotypeSummary.1.gz
+share/man/man1/hapLrt.1.gz
+share/man/man1/iHS.1.gz
+share/man/man1/meltEHH.1.gz
+share/man/man1/normalize-iHS.1.gz
+share/man/man1/pFst.1.gz
+share/man/man1/pVst.1.gz
+share/man/man1/permuteGPAT++.1.gz
+share/man/man1/permuteSmooth.1.gz
+share/man/man1/plotHaps.1.gz
+share/man/man1/popStats.1.gz
+share/man/man1/pyvcflib.1.gz
+share/man/man1/segmentFst.1.gz
+share/man/man1/segmentIhs.1.gz
+share/man/man1/sequenceDiversity.1.gz
+share/man/man1/smoother.1.gz
+share/man/man1/vcf2dag.1.gz
+share/man/man1/vcf2fasta.1.gz
+share/man/man1/vcf2tsv.1.gz
+share/man/man1/vcfaddinfo.1.gz
+share/man/man1/vcfafpath.1.gz
+share/man/man1/vcfallelicprimitives.1.gz
+share/man/man1/vcfaltcount.1.gz
+share/man/man1/vcfannotate.1.gz
+share/man/man1/vcfannotategenotypes.1.gz
+share/man/man1/vcfbreakmulti.1.gz
+share/man/man1/vcfcat.1.gz
+share/man/man1/vcfcheck.1.gz
+share/man/man1/vcfclassify.1.gz
+share/man/man1/vcfcleancomplex.1.gz
+share/man/man1/vcfcombine.1.gz
+share/man/man1/vcfcommonsamples.1.gz
+share/man/man1/vcfcountalleles.1.gz
+share/man/man1/vcfcreatemulti.1.gz
+share/man/man1/vcfdistance.1.gz
+share/man/man1/vcfecho.1.gz
+share/man/man1/vcfentropy.1.gz
+share/man/man1/vcfevenregions.1.gz
+share/man/man1/vcffilter.1.gz
+share/man/man1/vcffixup.1.gz
+share/man/man1/vcfflatten.1.gz
+share/man/man1/vcfgeno2alleles.1.gz
+share/man/man1/vcfgeno2haplo.1.gz
+share/man/man1/vcfgenosamplenames.1.gz
+share/man/man1/vcfgenosummarize.1.gz
+share/man/man1/vcfgenotypecompare.1.gz
+share/man/man1/vcfgenotypes.1.gz
+share/man/man1/vcfglbound.1.gz
+share/man/man1/vcfglxgt.1.gz
+share/man/man1/vcfhetcount.1.gz
+share/man/man1/vcfhethomratio.1.gz
+share/man/man1/vcfindex.1.gz
+share/man/man1/vcfinfo2qual.1.gz
+share/man/man1/vcfinfosummarize.1.gz
+share/man/man1/vcfintersect.1.gz
+share/man/man1/vcfkeepgeno.1.gz
+share/man/man1/vcfkeepinfo.1.gz
+share/man/man1/vcfkeepsamples.1.gz
+share/man/man1/vcfld.1.gz
+share/man/man1/vcfleftalign.1.gz
+share/man/man1/vcflength.1.gz
+share/man/man1/vcflib-api.1.gz
+share/man/man1/vcflib.1.gz
+share/man/man1/vcfnulldotslashdot.1.gz
+share/man/man1/vcfnullgenofields.1.gz
+share/man/man1/vcfnumalt.1.gz
+share/man/man1/vcfoverlay.1.gz
+share/man/man1/vcfparsealts.1.gz
+share/man/man1/vcfprimers.1.gz
+share/man/man1/vcfqual2info.1.gz
+share/man/man1/vcfrandom.1.gz
+share/man/man1/vcfrandomsample.1.gz
+share/man/man1/vcfremap.1.gz
+share/man/man1/vcfremoveaberrantgenotypes.1.gz
+share/man/man1/vcfremovesamples.1.gz
+share/man/man1/vcfroc.1.gz
+share/man/man1/vcfsample2info.1.gz
+share/man/man1/vcfsamplediff.1.gz
+share/man/man1/vcfsamplenames.1.gz
+share/man/man1/vcfsitesummarize.1.gz
+share/man/man1/vcfstats.1.gz
+share/man/man1/vcfstreamsort.1.gz
+share/man/man1/vcfuniq.1.gz
+share/man/man1/vcfuniqalleles.1.gz
+share/man/man1/vcfwave.1.gz
+share/man/man1/wcFst.1.gz