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Bump library versions
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Isaac Turner committed Dec 7, 2018
1 parent b518520 commit b8fceaa
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Showing 3 changed files with 3 additions and 3 deletions.
2 changes: 1 addition & 1 deletion libs/bcftools
Submodule bcftools updated 77 files
+8 −0 call.h
+14 −6 consensus.c
+176 −10 convert.c
+143 −30 csq.c
+96 −48 doc/bcftools.1
+64 −52 doc/bcftools.html
+32 −20 doc/bcftools.txt
+49 −14 filter.c
+19 −10 mcall.c
+1 −1 misc/demo-flt.pl
+1 −1 misc/plot-roh.py
+2 −2 mpileup.c
+5 −5 plugins/fill-tags.c
+376 −0 plugins/gvcfz.c
+124 −13 plugins/trio-stats.c
+1 −1 test/consensus3.2.out
+1 −1 test/consensus3.out
+11 −0 test/consensus4.out
+14 −0 test/consensus4.vcf
+5,307 −0 test/csq/ENST00000263103-INS/ENST00000263103-INS.fa
+1 −0 test/csq/ENST00000263103-INS/ENST00000263103-INS.fa.fai
+44 −0 test/csq/ENST00000263103-INS/ENST00000263103-INS.gff
+21 −0 test/csq/ENST00000263103-INS/insertions.txt
+15 −0 test/csq/ENST00000263103-INS/insertions.vcf
+331 −0 test/csq/ENST00000420190/ENST00000420190.fa
+1 −0 test/csq/ENST00000420190/ENST00000420190.fa.fai
+15 −0 test/csq/ENST00000420190/ENST00000420190.gff
+4 −0 test/csq/ENST00000420190/abort-in-csq-push.txt
+10 −0 test/csq/ENST00000420190/abort-in-csq-push.vcf
+2 −2 test/fill-tags-hemi.1.out
+2 −2 test/fill-tags-hemi.2.out
+20 −0 test/fill-tags-hwe.out
+9 −0 test/fill-tags-hwe.vcf
+7 −0 test/gvcfz.1.out
+7 −0 test/gvcfz.2.1.out
+25 −0 test/gvcfz.2.out
+2,627 −0 test/gvcfz.2.vcf
+2,630 −0 test/gvcfz.vcf
+4 −0 test/mpileup.3.tab
+275 −0 test/mpileup.3.vcf
+5 −0 test/mpileup.4.tab
+97 −0 test/mpileup.4.vcf
+6 −0 test/mpileup.5.tab
+576 −0 test/mpileup.5.vcf
+18 −0 test/mpileup.6.tab
+15 −0 test/mpileup.7.tab
+20 −0 test/mpileup.cAls.3.out
+21 −0 test/mpileup.cAls.4.out
+22 −0 test/mpileup.cAls.5.out
+38 −0 test/mpileup.cAls.6.out
+61 −0 test/mpileup.cAls.7.out
+2 −2 test/mpileup/indel-AD.1.out
+2 −2 test/mpileup/mpileup.1.out
+2 −2 test/mpileup/mpileup.10.out
+2 −2 test/mpileup/mpileup.11.out
+2 −2 test/mpileup/mpileup.2.out
+2 −2 test/mpileup/mpileup.3.out
+2 −2 test/mpileup/mpileup.4.out
+2 −2 test/mpileup/mpileup.5.out
+2 −2 test/mpileup/mpileup.6.out
+2 −2 test/mpileup/mpileup.7.out
+2 −2 test/mpileup/mpileup.8.out
+2 −2 test/mpileup/mpileup.9.out
+14 −0 test/norm.rmdup.2.1.out
+11 −0 test/norm.rmdup.2.2.out
+14 −0 test/norm.rmdup.2.vcf
+3 −0 test/query.63.out
+13 −0 test/query.64.out
+12 −0 test/query.65.out
+19 −0 test/query.pbinom.1.vcf
+21 −2 test/test.pl
+4 −4 test/trio-stats.out
+1 −0 test/trio-stats.vcf
+220 −23 vcfcall.c
+11 −3 vcffilter.c
+29 −22 vcfnorm.c
+6 −7 vcfsort.c
2 changes: 1 addition & 1 deletion libs/htslib
Submodule htslib updated 54 files
+1 −0 .gitignore
+38 −19 .travis.yml
+10 −5 Makefile
+13 −0 NEWS
+4 −0 README.md
+8 −0 bgzf.c
+65 −18 cram/cram_encode.c
+5 −2 cram/cram_index.c
+6 −1 cram/cram_io.c
+1 −0 cram/cram_structs.h
+36 −29 cram/open_trace_file.c
+39 −2 hfile.c
+3 −0 hfile_libcurl.c
+33 −17 hts.c
+3 −10 htslib/bgzf.h
+17 −1 htslib/hfile.h
+1 −1 htslib/hts.h
+1 −1 htslib/kseq.h
+1 −1 htslib/kstring.h
+46 −15 htslib/sam.h
+2 −0 realn.c
+121 −22 sam.c
+18 −1 test/compare_sam.pl
+25 −1 test/hfile.c
+10 −0 test/mpileup/c1#pad1.out
+47 −0 test/mpileup/c1#pad1.sam
+10 −0 test/mpileup/c1#pad2.out
+55 −0 test/mpileup/c1#pad2.sam
+5 −0 test/mpileup/c1#pad3.out
+53 −0 test/mpileup/c1#pad3.sam
+11 −0 test/mpileup/mp_D.out
+36 −0 test/mpileup/mp_D.sam
+12 −0 test/mpileup/mp_DI.out
+40 −0 test/mpileup/mp_DI.sam
+11 −0 test/mpileup/mp_I.out
+41 −0 test/mpileup/mp_I.sam
+12 −0 test/mpileup/mp_ID.out
+45 −0 test/mpileup/mp_ID.sam
+11 −0 test/mpileup/mp_N.out
+40 −0 test/mpileup/mp_N.sam
+13 −0 test/mpileup/mp_N2.out
+46 −0 test/mpileup/mp_N2.sam
+10 −0 test/mpileup/mp_P.out
+41 −0 test/mpileup/mp_P.sam
+71 −0 test/mpileup/mpileup.tst
+34 −0 test/mpileup/test-pileup.sh
+248 −0 test/pileup.c
+189 −0 test/simple_test_driver.sh
+3 −151 test/tabix/test-tabix.sh
+70 −0 test/test.pl
+22 −0 test/xx#MD.sam
+20 −0 test/xx#MD2.sam
+2 −0 test/xx.fa
+1 −0 test/xx.fa.fai
2 changes: 1 addition & 1 deletion libs/samtools
Submodule samtools updated 17 files
+23 −3 .travis.yml
+5 −5 Makefile
+9 −0 NEWS
+4 −0 README.md
+2 −2 bam_md.c
+154 −92 bam_split.c
+1 −1 bam_tview.h
+1 −1 configure.ac
+7 −2 doc/samtools-split.1
+4 −1 doc/samtools-view.1
+88 −18 stats.c
+20 −2 stats_isize.c
+41 −0 test/split/split.expected.grp1.sam
+41 −0 test/split/split.expected.grp2.sam
+34 −0 test/split/split.expected.unk.sam
+62 −0 test/split/split.sam
+29 −1 test/test.pl

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