[med-svn] [libvcflib] branch master updated (9fa4de4 -> d56d53d)
Andreas Tille
tille at debian.org
Wed Jun 22 15:05:02 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository libvcflib.
from 9fa4de4 Libtabixpp is now available but some other things (smithwaterman) are missing
new dfbb48a cme fix dpkg-control
new 42313f6 Imported Upstream version 1.0.0~rc1
new 60301a3 Merge tag 'upstream/1.0.0_rc1'
new 00c3fdd New upstream release candidate
new 136e5b5 Adapt patches
new bdcf5e1 Use debian packaged libsmithwatermann
new d56d53d Use pkg-config to find smithwatermann header file
The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.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 -
debian/changelog | 2 +-
debian/control | 16 +-
debian/patches/ignore_smith_watermann.patch | 55 +
debian/patches/series | 1 +
debian/patches/use_debian_packaged_tabixpp.patch | 51 +-
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 +
140 files changed, 228639 insertions(+), 1923 deletions(-)
create mode 100644 .travis.yml
create mode 100644 1KG_Index/1KG_IDs.txt
create mode 100755 1KG_Index/1kG_ethnic_index.py
create mode 100644 1KG_Index/README
copy Makefile => Makefile.old (98%)
delete mode 100755 bin/bed2region
create mode 100755 bin/plotBfst.R
create mode 100755 bin/plotHapLrt.R
create mode 100755 bin/plotHaplotypes.R
create mode 100755 bin/plotPfst.R
create mode 100755 bin/plotSmoothed.R
create mode 100755 bin/plotWCfst.R
create mode 100755 bin/plotXPEHH.R
delete mode 100755 bin/plot_roc.r
delete mode 100755 bin/vcf2bed.py
delete mode 100755 bin/vcf2sqlite.py
delete mode 100755 bin/vcf_strip_extra_headers
delete mode 100755 bin/vcfbiallelic
delete mode 100755 bin/vcfclearid
delete mode 100755 bin/vcfclearinfo
delete mode 100755 bin/vcfcomplex
delete mode 100755 bin/vcffirstheader
delete mode 100755 bin/vcfgtcompare.sh
delete mode 100755 bin/vcfindelproximity
delete mode 100755 bin/vcfindels
delete mode 100755 bin/vcfmultiallelic
delete mode 100755 bin/vcfmultiway
delete mode 100755 bin/vcfmultiwayscripts
delete mode 100755 bin/vcfnobiallelicsnps
delete mode 100755 bin/vcfnoindels
delete mode 100755 bin/vcfnosnps
delete mode 100755 bin/vcfnulldotslashdot
delete mode 100755 bin/vcfplotaltdiscrepancy.r
delete mode 100755 bin/vcfplotaltdiscrepancy.sh
delete mode 100755 bin/vcfplotsitediscrepancy.r
delete mode 100755 bin/vcfplottstv.sh
delete mode 100755 bin/vcfprintaltdiscrepancy.r
delete mode 100755 bin/vcfprintaltdiscrepancy.sh
delete mode 100755 bin/vcfqualfilter
delete mode 100755 bin/vcfregionreduce
delete mode 100755 bin/vcfregionreduce_and_cut
delete mode 100755 bin/vcfregionreduce_pipe
delete mode 100755 bin/vcfregionreduce_uncompressed
delete mode 100755 bin/vcfremovenonATGC
delete mode 100755 bin/vcfsnps
delete mode 100755 bin/vcfsort
delete mode 100755 bin/vcfvarstats
create mode 100644 debian/patches/ignore_smith_watermann.patch
create mode 100644 examples/612.bFst_SatApr12_12_29_17.png
create mode 100644 examples/612.counts_FriApr11_13_16_42.png
create mode 100644 examples/612.nocounts.smoothed_TueApr15_13_25_53.png
create mode 100644 examples/612.nocounts_FriApr11_13_16_38.png
create mode 100644 examples/612.wcfst.txt_FriApr11_13_17_02.png
create mode 100644 examples/example-ehh.png
create mode 100644 examples/headCrest.haps.txt_ThuMay29_15_08_53.pdf
create mode 100644 examples/headCrest.haps.txt_ThuMay29_15_08_53.png
create mode 100644 examples/phasing-diff-res.png
create mode 100644 examples/phasing-results.png
create mode 100644 examples/scaffold612.d-stat.10kb.txt_abba-baba_WedOct29_10_17_10.png
create mode 100644 examples/t.hapass.txt_TueJun24_11_52_08.png
create mode 100644 examples/xp-phased.txt
create mode 100644 examples/xp-phased.txt_TueApr29_13_20_47.png
create mode 100644 examples/xp-unphased.txt
create mode 100644 examples/xp-unphased.txt_TueApr29_13_20_58.png
create mode 100644 examples/xpehh_WedApr23_11_30_10.png
create mode 100644 logos/websiteLogo.pdf
create mode 100644 logos/websiteLogo.png
create mode 100644 paper/Fig1.pdf
create mode 100644 paper/Fig2.pdf
create mode 100644 paper/PLOS-submission-eps-converted-to.pdf
create mode 100755 paper/PLOS-submission.eps
create mode 100755 paper/plos2015.bst
create mode 100644 paper/plos_latex_template.aux
create mode 100644 paper/plos_latex_template.bbl
create mode 100644 paper/plos_latex_template.blg
create mode 100644 paper/plos_latex_template.log
create mode 100644 paper/plos_latex_template.out
create mode 100644 paper/plos_latex_template.pdf
create mode 100644 paper/plos_latex_template.synctex.gz
create mode 100755 paper/plos_latex_template.tex
create mode 100644 samples/scaffold612.phased.vcf
create mode 100644 samples/scaffold612.vcf
create mode 100644 src/LD.cpp
create mode 100644 src/abba-baba.cpp
create mode 100644 src/bFst.cpp
create mode 100644 src/cdflib.cpp
create mode 100644 src/cdflib.hpp
create mode 100644 src/dumpContigsFromHeader.cpp
create mode 100644 src/genotypeSummary.cpp
create mode 100644 src/gl-XPEHH.cpp
create mode 100644 src/gpatInfo.hpp
create mode 100644 src/hapLrt.cpp
create mode 100644 src/iHS.cpp
create mode 100644 src/meltEHH.cpp
create mode 100644 src/normalize-iHS.cpp
create mode 100644 src/pFst.cpp
create mode 100644 src/pdflib.cpp
create mode 100644 src/pdflib.hpp
create mode 100644 src/permuteGPAT++.cpp
create mode 100644 src/permuteGPATsmoother.cpp
create mode 100644 src/permuteRegions.cpp
create mode 100644 src/permuteSmooth.cpp
create mode 100644 src/plotHaps.cpp
create mode 100644 src/popStats.cpp
create mode 100644 src/rnglib.cpp
create mode 100644 src/rnglib.hpp
create mode 100644 src/segmentFst.cpp
create mode 100644 src/segmentIhs.cpp
create mode 100644 src/sequenceDiversity.cpp
create mode 100644 src/smoother.cpp
create mode 100644 src/splitUniqStarts.cpp
create mode 100644 src/var.cpp
create mode 100644 src/var.hpp
create mode 100644 src/vcfToHap.cpp
create mode 100644 src/wcFst.cpp
create mode 100644 src/xpEHH.cpp
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