[med-svn] [libvcflib] 03/07: Merge tag 'upstream/1.0.0_rc1'
Andreas Tille
tille at debian.org
Wed Jun 22 15:05:12 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libvcflib.
commit 60301a3a83924e292b3446c85183165c4d8d2078
Merge: dfbb48a 42313f6
Author: Andreas Tille <tille at debian.org>
Date: Mon Jun 20 09:57:06 2016 +0200
Merge tag 'upstream/1.0.0_rc1'
Upstream version 1.0.0~rc1
.gitignore | 4 +
.travis.yml | 11 +
1KG_Index/1KG_IDs.txt | 3500 +
1KG_Index/1kG_ethnic_index.py | 54 +
1KG_Index/README | 1 +
Makefile | 96 +-
Makefile => Makefile.old | 2 +-
README.md | 273 +-
bin/bed2region | 9 -
bin/plotBfst.R | 15 +
bin/plotHapLrt.R | 14 +
bin/plotHaplotypes.R | 27 +
bin/plotPfst.R | 15 +
bin/plotSmoothed.R | 28 +
bin/plotWCfst.R | 14 +
bin/plotXPEHH.R | 14 +
bin/plot_roc.r | 153 -
bin/vcf2bed.py | 16 -
bin/vcf2sqlite.py | 130 -
bin/vcf_strip_extra_headers | 18 -
bin/vcfbiallelic | 20 -
bin/vcfclearid | 12 -
bin/vcfclearinfo | 12 -
bin/vcfcomplex | 26 -
bin/vcffirstheader | 16 -
bin/vcfgtcompare.sh | 16 -
bin/vcfindelproximity | 82 -
bin/vcfindels | 26 -
bin/vcfmultiallelic | 20 -
bin/vcfmultiway | 20 -
bin/vcfmultiwayscripts | 30 -
bin/vcfnobiallelicsnps | 29 -
bin/vcfnoindels | 25 -
bin/vcfnosnps | 25 -
bin/vcfnulldotslashdot | 22 -
bin/vcfplotaltdiscrepancy.r | 511 -
bin/vcfplotaltdiscrepancy.sh | 12 -
bin/vcfplotsitediscrepancy.r | 99 -
bin/vcfplottstv.sh | 13 -
bin/vcfprintaltdiscrepancy.r | 37 -
bin/vcfprintaltdiscrepancy.sh | 18 -
bin/vcfqualfilter | 32 -
bin/vcfregionreduce | 29 -
bin/vcfregionreduce_and_cut | 32 -
bin/vcfregionreduce_pipe | 29 -
bin/vcfregionreduce_uncompressed | 29 -
bin/vcfremovenonATGC | 29 -
bin/vcfsnps | 26 -
bin/vcfsort | 3 -
bin/vcfvarstats | 225 -
examples/612.bFst_SatApr12_12_29_17.png | Bin 0 -> 214348 bytes
examples/612.counts_FriApr11_13_16_42.png | Bin 0 -> 89401 bytes
.../612.nocounts.smoothed_TueApr15_13_25_53.png | Bin 0 -> 374112 bytes
examples/612.nocounts_FriApr11_13_16_38.png | Bin 0 -> 89270 bytes
examples/612.wcfst.txt_FriApr11_13_17_02.png | Bin 0 -> 110860 bytes
examples/example-ehh.png | Bin 0 -> 168466 bytes
examples/headCrest.haps.txt_ThuMay29_15_08_53.pdf | Bin 0 -> 52006 bytes
examples/headCrest.haps.txt_ThuMay29_15_08_53.png | Bin 0 -> 127323 bytes
examples/phasing-diff-res.png | Bin 0 -> 7136 bytes
examples/phasing-results.png | Bin 0 -> 8177 bytes
...d-stat.10kb.txt_abba-baba_WedOct29_10_17_10.png | Bin 0 -> 132377 bytes
examples/t.hapass.txt_TueJun24_11_52_08.png | Bin 0 -> 92866 bytes
examples/xp-phased.txt | 15712 ++++
examples/xp-phased.txt_TueApr29_13_20_47.png | Bin 0 -> 152427 bytes
examples/xp-unphased.txt | 15762 ++++
examples/xp-unphased.txt_TueApr29_13_20_58.png | Bin 0 -> 114144 bytes
examples/xpehh_WedApr23_11_30_10.png | Bin 0 -> 94758 bytes
logos/websiteLogo.pdf | 1590 +
logos/websiteLogo.png | Bin 0 -> 4144 bytes
paper/Fig1.pdf | 2916 +
paper/Fig2.pdf | 77171 +++++++++++++++++++
paper/PLOS-submission-eps-converted-to.pdf | Bin 0 -> 15274 bytes
paper/PLOS-submission.eps | Bin 0 -> 283246 bytes
paper/plos2015.bst | 1882 +
paper/plos_latex_template.aux | 61 +
paper/plos_latex_template.bbl | 3 +
paper/plos_latex_template.blg | 65 +
paper/plos_latex_template.log | 1148 +
paper/plos_latex_template.out | 0
paper/plos_latex_template.pdf | Bin 0 -> 221858 bytes
paper/plos_latex_template.synctex.gz | Bin 0 -> 50963 bytes
paper/plos_latex_template.tex | 439 +
samples/scaffold612.phased.vcf | 21068 +++++
samples/scaffold612.vcf | 59968 ++++++++++++++
src/BedReader.h | 2 +-
src/LD.cpp | 422 +
src/Variant.cpp | 20 +-
src/Variant.h | 10 +-
src/abba-baba.cpp | 313 +
src/bFst.cpp | 621 +
src/cdflib.cpp | 10873 +++
src/cdflib.hpp | 128 +
src/dumpContigsFromHeader.cpp | 47 +
src/genotypeSummary.cpp | 318 +
src/gl-XPEHH.cpp | 692 +
src/gpatInfo.hpp | 32 +
src/hapLrt.cpp | 624 +
src/iHS.cpp | 642 +
src/meltEHH.cpp | 631 +
src/normalize-iHS.cpp | 302 +
src/pFst.cpp | 368 +
src/pdflib.cpp | 3478 +
src/pdflib.hpp | 47 +
src/permuteGPAT++.cpp | 223 +
src/permuteGPATsmoother.cpp | 223 +
src/permuteRegions.cpp | 402 +
src/permuteSmooth.cpp | 425 +
src/plotHaps.cpp | 371 +
src/popStats.cpp | 268 +
src/rnglib.cpp | 1807 +
src/rnglib.hpp | 32 +
src/segmentFst.cpp | 295 +
src/segmentIhs.cpp | 295 +
src/sequenceDiversity.cpp | 462 +
src/smoother.cpp | 376 +
src/splitUniqStarts.cpp | 230 +
src/var.cpp | 388 +
src/var.hpp | 115 +
src/vcf2dag.cpp | 4 +-
src/vcf2fasta.cpp | 2 +-
src/vcfToHap.cpp | 455 +
src/vcfcheck.cpp | 2 +-
src/vcfcombine.cpp | 4 +
src/vcfentropy.cpp | 2 +-
src/vcfevenregions.cpp | 2 +-
src/vcfgeno2haplo.cpp | 2 +-
src/vcfinfosummarize.cpp | 2 +-
src/vcfintersect.cpp | 4 +-
src/vcfleftalign.cpp | 2 +-
src/vcfprimers.cpp | 2 +-
src/vcfremap.cpp | 4 +-
src/vcfroc.cpp | 4 +-
src/vcfsample2info.cpp | 2 +-
src/wcFst.cpp | 332 +
src/xpEHH.cpp | 446 +
135 files changed, 228557 insertions(+), 1880 deletions(-)
--
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