[med-svn] [bcftools] 02/06: Merge tag 'upstream/1.4.1'

Andreas Tille tille at debian.org
Sun Jun 18 20:00:10 UTC 2017


This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository bcftools.

commit 7f0275f5d4676a435dcd288a3c2ef07b10b98b8f
Merge: f9a9e80 0fb5584
Author: Andreas Tille <tille at debian.org>
Date:   Sun Jun 18 21:40:20 2017 +0200

    Merge tag 'upstream/1.4.1'
    
    Upstream version 1.4.1

 HMM.c                                              |  141 +-
 HMM.h                                              |   26 +-
 INSTALL                                            |   24 +-
 Makefile                                           |   95 +-
 NEWS                                               |  236 +
 bam2bcf.c                                          |  857 +++
 bam2bcf.h                                          |  138 +
 bam2bcf_indel.c                                    |  470 ++
 bam_sample.c                                       |  393 ++
 bam_sample.h                                       |   50 +
 bcftools.h                                         |    1 +
 bin.c                                              |  104 +
 bin.h                                              |   65 +
 call.h                                             |    3 +-
 ccall.c                                            |   10 +-
 consensus.c                                        |   56 +-
 convert.c                                          |  490 +-
 csq.c                                              | 3824 +++++++++++++
 doc/bcftools.1                                     | 1403 ++++-
 doc/bcftools.html                                  |  919 +++-
 doc/bcftools.txt                                   |  989 +++-
 filter.c                                           |  357 +-
 hclust.c                                           |  400 ++
 hclust.h                                           |   77 +
 kheap.h                                            |  171 +
 main.c                                             |   10 +
 mcall.c                                            |  228 +-
 {plugins => misc}/color-chrs.pl                    |    0
 misc/guess-ploidy.py                               |  117 +
 misc/plot-roh.py                                   |  253 +
 plot-vcfstats => misc/plot-vcfstats                |  294 +-
 misc/run-roh.pl                                    |  308 ++
 vcfutils.pl => misc/vcfutils.pl                    |    0
 mpileup.c                                          | 1110 ++++
 mw.h                                               | 1944 +++++++
 ploidy.c                                           |   22 +-
 ploidy.h                                           |    2 +-
 plugins/GTsubset.c                                 |  266 +
 plugins/GTsubset.mk                                |    2 +
 plugins/ad-bias.c                                  |  226 +
 plugins/ad-bias.mk                                 |    2 +
 plugins/af-dist.c                                  |  220 +
 plugins/af-dist.mk                                 |    2 +
 plugins/check-sparsity.c                           |  273 +
 plugins/color-chrs.c                               |    4 +-
 plugins/fill-from-fasta.c                          |  206 +
 plugins/fill-from-fasta.mk                         |    2 +
 plugins/fill-tags.c                                |  545 +-
 plugins/fixploidy.c                                |    1 +
 plugins/fixref.c                                   |  576 ++
 plugins/guess-ploidy.c                             |  568 ++
 plugins/impute-info.c                              |    2 +
 plugins/isecGT.c                                   |  177 +
 plugins/mendelian.c                                |   12 +-
 plugins/setGT.c                                    |  148 +-
 plugins/setGT.mk                                   |    2 +
 plugins/tag2tag.c                                  |  146 +-
 plugins/trio-switch-rate.c                         |  273 +
 plugins/vcf2sex.c                                  |  511 --
 plugins/vcf2sex.mk                                 |    2 -
 prob1.c                                            |   12 +-
 prob1.h                                            |    2 +-
 regidx.c                                           |  598 ++
 regidx.h                                           |  191 +
 reheader.c                                         |    6 +-
 smpl_ilist.c                                       |  106 +
 smpl_ilist.h                                       |   47 +
 tabix.c                                            |   30 +-
 test/aa.fa                                         |   29 +
 test/aa.fa.fai                                     |    8 +
 test/aa.hdr                                        |    1 +
 test/aa.out                                        |   31 +
 test/aa.vcf                                        |   30 +
 test/ad-bias.out                                   |   25 +
 test/ad-bias.samples                               |    2 +
 test/ad-bias.vcf                                   |   42 +
 test/af-dist.out                                   |   23 +
 test/af-dist.vcf                                   |   19 +
 test/annotate11.out                                |   18 +
 test/annotate12.out                                |   20 +
 test/annotate13.out                                |   15 +
 test/annots11.tab                                  |    4 +
 test/check.chk                                     |   12 +-
 test/check_merge.chk                               |    6 +-
 test/csq.1.out                                     |   99 +
 test/csq.fa                                        |   34 +
 test/csq.fa.fai                                    |    3 +
 test/csq.gff3                                      |   40 +
 test/csq.vcf                                       |   40 +
 test/csq/ENSG00000173376/ENSG00000173376.fa        |  626 +++
 test/csq/ENSG00000173376/ENSG00000173376.fa.fai    |    1 +
 test/csq/ENSG00000173376/ENSG00000173376.gff       |   22 +
 test/csq/ENSG00000173376/synon.txt                 |    3 +
 test/csq/ENSG00000173376/synon.vcf                 |    7 +
 test/csq/ENST00000218032/ENST00000218032.fa        |  278 +
 test/csq/ENST00000218032/ENST00000218032.fa.fai    |    1 +
 test/csq/ENST00000218032/ENST00000218032.gff       |    8 +
 test/csq/ENST00000218032/start-lost.txt            |    3 +
 test/csq/ENST00000218032/start-lost.txt-l          |    3 +
 test/csq/ENST00000218032/start-lost.vcf            |    6 +
 test/csq/ENST00000227471/ENST00000227471.fa        |  233 +
 test/csq/ENST00000227471/ENST00000227471.fa.fai    |    1 +
 test/csq/ENST00000227471/ENST00000227471.gff       |   28 +
 .../insert-splice-vs-frameshift.txt                |    3 +
 .../insert-splice-vs-frameshift.vcf                |    7 +
 test/csq/ENST00000256452/ENST00000256452.fa        |  953 ++++
 test/csq/ENST00000256452/ENST00000256452.fa.fai    |    1 +
 test/csq/ENST00000256452/ENST00000256452.gff       |   30 +
 test/csq/ENST00000256452/intron.txt                |    3 +
 test/csq/ENST00000256452/intron.vcf                |    7 +
 test/csq/ENST00000294661/ENST00000294661.fa        |  163 +
 test/csq/ENST00000294661/ENST00000294661.fa.fai    |    1 +
 test/csq/ENST00000294661/ENST00000294661.gff       |    6 +
 test/csq/ENST00000294661/non-coding-boundary.txt   |    3 +
 test/csq/ENST00000294661/non-coding-boundary.txt-l |    3 +
 test/csq/ENST00000294661/non-coding-boundary.vcf   |    6 +
 test/csq/ENST00000295641/ENST00000295641.fa        |  312 ++
 test/csq/ENST00000295641/ENST00000295641.fa.fai    |    1 +
 test/csq/ENST00000295641/ENST00000295641.gff       |   54 +
 test/csq/ENST00000295641/not-a-start-lost.txt      |    3 +
 test/csq/ENST00000295641/not-a-start-lost.txt-l    |    3 +
 test/csq/ENST00000295641/not-a-start-lost.vcf      |    6 +
 test/csq/ENST00000301246/15bp-insert.txt           |    3 +
 test/csq/ENST00000301246/15bp-insert.vcf           |    7 +
 test/csq/ENST00000301246/ENST00000301246.fa        |   16 +
 test/csq/ENST00000301246/ENST00000301246.fa.fai    |    1 +
 test/csq/ENST00000301246/ENST00000301246.gff       |   23 +
 test/csq/ENST00000303039/ENST00000303039.fa        |   19 +
 test/csq/ENST00000303039/ENST00000303039.fa.fai    |    1 +
 test/csq/ENST00000303039/ENST00000303039.gff       |    6 +
 test/csq/ENST00000303039/not-a-stop.txt            |    3 +
 test/csq/ENST00000303039/not-a-stop.txt-l          |    3 +
 test/csq/ENST00000303039/not-a-stop.vcf            |    6 +
 test/csq/ENST00000318249/ENST00000318249.fa        |  749 +++
 test/csq/ENST00000318249/ENST00000318249.fa.fai    |    1 +
 test/csq/ENST00000318249/ENST00000318249.gff       |   34 +
 test/csq/ENST00000318249/ascii-art.txt             |    9 +
 test/csq/ENST00000318249/start-lost.txt            |    3 +
 test/csq/ENST00000318249/start-lost.txt-l          |    3 +
 test/csq/ENST00000318249/start-lost.vcf            |    6 +
 test/csq/ENST00000318249/start-lost.vcf.ori        |    5 +
 test/csq/ENST00000318249/start-lost.vep            |   14 +
 test/csq/ENST00000329454/ENST00000329454.fa        |   78 +
 test/csq/ENST00000329454/ENST00000329454.fa.fai    |    1 +
 test/csq/ENST00000329454/ENST00000329454.gff       |    8 +
 test/csq/ENST00000329454/boundary-deletion.txt     |    3 +
 test/csq/ENST00000329454/boundary-deletion.txt-l   |    3 +
 test/csq/ENST00000329454/boundary-deletion.vcf     |    6 +
 test/csq/ENST00000341065/ENST00000341065.fa        |  330 ++
 test/csq/ENST00000341065/ENST00000341065.fa.fai    |    1 +
 test/csq/ENST00000341065/ENST00000341065.gff       |   27 +
 test/csq/ENST00000341065/ascii-art.txt             |   61 +
 test/csq/ENST00000341065/ascii-art.txt-l           |   61 +
 test/csq/ENST00000341065/frame1.txt                |    3 +
 test/csq/ENST00000341065/frame1.txt-l              |    3 +
 test/csq/ENST00000341065/frame1.vcf                |    6 +
 test/csq/ENST00000341065/frame2.txt                |    3 +
 test/csq/ENST00000341065/frame2.txt-l              |    3 +
 test/csq/ENST00000341065/frame2.vcf                |    7 +
 test/csq/ENST00000341065/frame3.txt                |    3 +
 test/csq/ENST00000341065/frame3.txt-l              |    3 +
 test/csq/ENST00000341065/frame3.vcf                |    6 +
 test/csq/ENST00000341065/not-a-start-lost.txt      |    3 +
 test/csq/ENST00000341065/not-a-start-lost.txt-l    |    3 +
 test/csq/ENST00000341065/not-a-start-lost.vcf      |    6 +
 .../csq/ENST00000341065/splice-acceptor-donor1.txt |   33 +
 .../ENST00000341065/splice-acceptor-donor1.txt-l   |   33 +
 .../csq/ENST00000341065/splice-acceptor-donor1.vcf |   16 +
 .../csq/ENST00000341065/splice-acceptor-donor2.txt |    3 +
 .../ENST00000341065/splice-acceptor-donor2.txt-l   |    3 +
 .../csq/ENST00000341065/splice-acceptor-donor2.vcf |    6 +
 .../csq/ENST00000341065/splice-acceptor-donor3.txt |    3 +
 .../ENST00000341065/splice-acceptor-donor3.txt-l   |    3 +
 .../csq/ENST00000341065/splice-acceptor-donor3.vcf |    6 +
 .../csq/ENST00000341065/splice-acceptor-donor4.txt |    3 +
 .../ENST00000341065/splice-acceptor-donor4.txt-l   |    3 +
 .../csq/ENST00000341065/splice-acceptor-donor4.vcf |    6 +
 .../csq/ENST00000341065/splice-acceptor-donor5.txt |    3 +
 .../ENST00000341065/splice-acceptor-donor5.txt-l   |    3 +
 .../csq/ENST00000341065/splice-acceptor-donor5.vcf |    6 +
 .../csq/ENST00000341065/splice-acceptor-donor6.txt |    3 +
 .../ENST00000341065/splice-acceptor-donor6.txt-l   |    3 +
 .../csq/ENST00000341065/splice-acceptor-donor6.vcf |    6 +
 .../csq/ENST00000341065/splice-acceptor-donor7.txt |    3 +
 .../ENST00000341065/splice-acceptor-donor7.txt-l   |    3 +
 .../csq/ENST00000341065/splice-acceptor-donor7.vcf |    6 +
 .../csq/ENST00000341065/splice-acceptor-donor8.txt |    3 +
 .../ENST00000341065/splice-acceptor-donor8.txt-l   |    3 +
 .../csq/ENST00000341065/splice-acceptor-donor8.vcf |    6 +
 .../csq/ENST00000341065/splice-acceptor-donor9.txt |    3 +
 .../ENST00000341065/splice-acceptor-donor9.txt-l   |    3 +
 .../csq/ENST00000341065/splice-acceptor-donor9.vcf |    6 +
 test/csq/ENST00000357367/ENST00000357367.fa        |   71 +
 test/csq/ENST00000357367/ENST00000357367.fa.fai    |    1 +
 test/csq/ENST00000357367/ENST00000357367.gff       |   12 +
 test/csq/ENST00000357367/stop-retained.txt         |    3 +
 test/csq/ENST00000357367/stop-retained.vcf         |    7 +
 test/csq/ENST00000368801/ENST00000368801.fa        |  204 +
 test/csq/ENST00000368801/ENST00000368801.fa.fai    |    1 +
 test/csq/ENST00000368801/ENST00000368801.gff       |   10 +
 test/csq/ENST00000368801/compound-lost.txt         |    9 +
 test/csq/ENST00000368801/compound-lost.vcf         |    9 +
 test/csq/ENST00000373833/ENST00000373833.fa        |  557 ++
 test/csq/ENST00000373833/ENST00000373833.fa.fai    |    1 +
 test/csq/ENST00000373833/ENST00000373833.gff       |   30 +
 test/csq/ENST00000373833/boundary-insertion.txt    |    3 +
 test/csq/ENST00000373833/boundary-insertion.txt-l  |    3 +
 test/csq/ENST00000373833/boundary-insertion.vcf    |    6 +
 test/csq/ENST00000375992/ENST00000375992.fa        |  112 +
 test/csq/ENST00000375992/ENST00000375992.fa.fai    |    1 +
 test/csq/ENST00000375992/ENST00000375992.gff       |    8 +
 .../incorrect-synon-del-not-start-lost.txt         |    3 +
 .../incorrect-synon-del-not-start-lost.vcf         |    7 +
 test/csq/ENST00000378322/ENST00000378322.fa        |  368 ++
 test/csq/ENST00000378322/ENST00000378322.fa.fai    |    1 +
 test/csq/ENST00000378322/ENST00000378322.gff       |   26 +
 test/csq/ENST00000378322/ascii-art.txt             |    9 +
 test/csq/ENST00000378322/ascii-art.txt-l           |    9 +
 test/csq/ENST00000378322/end-overlap-tscript.txt   |    9 +
 test/csq/ENST00000378322/end-overlap-tscript.txt-l |    9 +
 test/csq/ENST00000378322/end-overlap-tscript.vcf   |    8 +
 test/csq/ENST00000381157/ENST00000381157.fa        |  903 +++
 test/csq/ENST00000381157/ENST00000381157.fa.fai    |    1 +
 test/csq/ENST00000381157/ENST00000381157.gff       |   14 +
 test/csq/ENST00000381157/haploid-diploid.txt       |    9 +
 test/csq/ENST00000381157/haploid-diploid.vcf       |   11 +
 test/csq/ENST00000382647/ENST00000382647.fa        |   52 +
 test/csq/ENST00000382647/ENST00000382647.fa.fai    |    1 +
 test/csq/ENST00000382647/ENST00000382647.gff       |    8 +
 .../ENST00000382647/synon-splice-region-insert.txt |    3 +
 .../ENST00000382647/synon-splice-region-insert.vcf |    7 +
 test/csq/ENST00000390520/ENST00000390520.fa        |    3 +
 test/csq/ENST00000390520/ENST00000390520.fa.fai    |    1 +
 test/csq/ENST00000390520/ENST00000390520.gff       |    4 +
 test/csq/ENST00000390520/deletion-overlap.txt      |    3 +
 test/csq/ENST00000390520/deletion-overlap.vcf      |    7 +
 test/csq/ENST00000409523/ENST00000409523.fa        | 1079 ++++
 test/csq/ENST00000409523/ENST00000409523.fa.fai    |    1 +
 test/csq/ENST00000409523/ENST00000409523.gff       |   16 +
 test/csq/ENST00000409523/ascii-art.txt             |   30 +
 test/csq/ENST00000409523/long-overlapping-del.txt  |    6 +
 test/csq/ENST00000409523/long-overlapping-del.vcf  |    8 +
 test/csq/ENST00000410009/ENST00000410009.fa        |   96 +
 test/csq/ENST00000410009/ENST00000410009.fa.fai    |    1 +
 test/csq/ENST00000410009/ENST00000410009.gff       |   16 +
 test/csq/ENST00000410009/ascii-art.txt             |    7 +
 test/csq/ENST00000410009/frameshift.txt            |    3 +
 test/csq/ENST00000410009/frameshift.vcf            |    7 +
 test/csq/ENST00000413103/ENST00000413103.fa        |   29 +
 test/csq/ENST00000413103/ENST00000413103.fa.fai    |    1 +
 test/csq/ENST00000413103/ENST00000413103.gff       |    4 +
 test/csq/ENST00000413103/long-deletion.txt         |    3 +
 test/csq/ENST00000413103/long-deletion.vcf         |    7 +
 test/csq/ENST00000420670/ENST00000420670.fa        | 2291 ++++++++
 test/csq/ENST00000420670/ENST00000420670.fa.fai    |    1 +
 test/csq/ENST00000420670/ENST00000420670.gff       |   11 +
 test/csq/ENST00000420670/start-stop-lost.txt       |    3 +
 test/csq/ENST00000420670/start-stop-lost.vcf       |    7 +
 test/csq/ENST00000423372/ENST00000423372.fa        |   76 +
 test/csq/ENST00000423372/ENST00000423372.fa.fai    |    1 +
 test/csq/ENST00000423372/ENST00000423372.gff       |    8 +
 test/csq/ENST00000423372/insert3.txt               |    6 +
 test/csq/ENST00000423372/insert3.txt-l             |    6 +
 test/csq/ENST00000423372/insert3.vcf               |    7 +
 test/csq/ENST00000423372/snps.txt                  |  117 +
 test/csq/ENST00000423372/snps.txt-l                |  117 +
 test/csq/ENST00000423372/snps.vcf                  |   45 +
 test/csq/ENST00000436063/ENST00000436063.fa        |  204 +
 test/csq/ENST00000436063/ENST00000436063.fa.fai    |    1 +
 test/csq/ENST00000436063/ENST00000436063.gff       |   18 +
 test/csq/ENST00000436063/insert-before-utr.txt     |    3 +
 test/csq/ENST00000436063/insert-before-utr.vcf     |    7 +
 test/csq/ENST00000448695/ENST00000448695.fa        | 2528 +++++++++
 test/csq/ENST00000448695/ENST00000448695.fa.fai    |    1 +
 test/csq/ENST00000448695/ENST00000448695.gff       |   55 +
 test/csq/ENST00000448695/syn-and-splice-reg.txt    |    3 +
 test/csq/ENST00000448695/syn-and-splice-reg.vcf    |    7 +
 test/csq/ENST00000479739/ENST00000479739.fa        |  813 +++
 test/csq/ENST00000479739/ENST00000479739.fa.fai    |    1 +
 test/csq/ENST00000479739/ENST00000479739.gff       |   26 +
 test/csq/ENST00000479739/short-cds-start-lost.txt  |    3 +
 .../csq/ENST00000479739/short-cds-start-lost.txt-l |    3 +
 test/csq/ENST00000479739/short-cds-start-lost.vcf  |    6 +
 test/csq/ENST00000519442/ENST00000519442.fa        |  766 +++
 test/csq/ENST00000519442/ENST00000519442.fa.fai    |    1 +
 test/csq/ENST00000519442/ENST00000519442.gff       |   16 +
 .../ENST00000519442/synon-splice-region-del.txt    |    3 +
 .../ENST00000519442/synon-splice-region-del.vcf    |    7 +
 test/csq/ENST00000520795/ENST00000520795.fa        | 4550 ++++++++++++++++
 test/csq/ENST00000520795/ENST00000520795.fa.fai    |    1 +
 test/csq/ENST00000520795/ENST00000520795.gff       |    8 +
 test/csq/ENST00000520795/ascii-art.txt             |    9 +
 test/csq/ENST00000520795/ascii-art.txt-l           |    9 +
 test/csq/ENST00000520795/long-inside-del.txt       |    3 +
 test/csq/ENST00000520795/long-inside-del.txt-l     |    3 +
 test/csq/ENST00000520795/long-inside-del.vcf       |    6 +
 test/csq/ENST00000520868/ENST00000520868.fa        |  621 +++
 test/csq/ENST00000520868/ENST00000520868.fa.fai    |    1 +
 test/csq/ENST00000520868/ENST00000520868.gff       |   15 +
 test/csq/ENST00000520868/ascii-art.txt             |    6 +
 test/csq/ENST00000520868/long-deletion.txt         |    3 +
 test/csq/ENST00000520868/long-deletion.vcf         |    7 +
 test/csq/ENST00000528237/ENST00000528237.fa        |  993 ++++
 test/csq/ENST00000528237/ENST00000528237.fa.fai    |    1 +
 test/csq/ENST00000528237/ENST00000528237.gff       |   17 +
 .../retained-stop-incomplete-cds.txt               |    3 +
 .../retained-stop-incomplete-cds.vcf               |    7 +
 test/csq/ENST00000536784/ENST00000536784.fa        |  259 +
 test/csq/ENST00000536784/ENST00000536784.fa.fai    |    1 +
 test/csq/ENST00000536784/ENST00000536784.gff       |    9 +
 test/csq/ENST00000536784/not-a-start-lost.txt      |    3 +
 test/csq/ENST00000536784/not-a-start-lost.txt-l    |    3 +
 test/csq/ENST00000536784/not-a-start-lost.vcf      |    6 +
 test/csq/ENST00000542803/ENST00000542803.fa        | 5726 ++++++++++++++++++++
 test/csq/ENST00000542803/ENST00000542803.fa.fai    |    1 +
 test/csq/ENST00000542803/ENST00000542803.gff       |   22 +
 test/csq/ENST00000542803/splice-region.txt         |    3 +
 test/csq/ENST00000542803/splice-region.txt-l       |    3 +
 test/csq/ENST00000542803/splice-region.vcf         |    6 +
 test/csq/ENST00000543077/ENST00000543077.fa        |  292 +
 test/csq/ENST00000543077/ENST00000543077.fa.fai    |    1 +
 test/csq/ENST00000543077/ENST00000543077.gff       |    7 +
 test/csq/ENST00000543077/not-a-start-lost.txt      |    3 +
 test/csq/ENST00000543077/not-a-start-lost.txt-l    |    3 +
 test/csq/ENST00000543077/not-a-start-lost.vcf      |    6 +
 test/csq/ENST00000545279/ENST00000545279.fa        |  934 ++++
 test/csq/ENST00000545279/ENST00000545279.fa.fai    |    1 +
 test/csq/ENST00000545279/ENST00000545279.gff       |   22 +
 test/csq/ENST00000545279/splice-region-insert.txt  |    3 +
 test/csq/ENST00000545279/splice-region-insert.vcf  |    7 +
 test/csq/ENST00000557788/ENST00000557788.fa        |   12 +
 test/csq/ENST00000557788/ENST00000557788.fa.fai    |    1 +
 test/csq/ENST00000557788/ENST00000557788.gff       |    6 +
 test/csq/ENST00000557788/ascii-art.txt             |    6 +
 test/csq/ENST00000557788/long-overlap-del.txt      |    3 +
 test/csq/ENST00000557788/long-overlap-del.vcf      |    7 +
 test/csq/ENST00000573314/ENST00000573314.fa        |  544 ++
 test/csq/ENST00000573314/ENST00000573314.fa.fai    |    1 +
 test/csq/ENST00000573314/ENST00000573314.gff       |   28 +
 test/csq/ENST00000573314/ascii-art.txt             |   16 +
 test/csq/ENST00000573314/ascii-art.txt-l           |   16 +
 .../incorrect-insertion-overlap.txt                |    3 +
 .../incorrect-insertion-overlap.txt-l              |    3 +
 .../incorrect-insertion-overlap.vcf                |    6 +
 test/csq/ENST00000593942/ENST00000593942.fa        |  345 ++
 test/csq/ENST00000593942/ENST00000593942.fa.fai    |    1 +
 test/csq/ENST00000593942/ENST00000593942.gff       |   18 +
 test/csq/ENST00000593942/last-codon-deletion.txt   |    3 +
 test/csq/ENST00000593942/last-codon-deletion.vcf   |    7 +
 test/csq/ENST00000624631/ENST00000624631.fa        |   25 +
 test/csq/ENST00000624631/ENST00000624631.fa.fai    |    1 +
 test/csq/ENST00000624631/ENST00000624631.gff       |    8 +
 test/csq/ENST00000624631/ambiguous.txt             |    3 +
 test/csq/ENST00000624631/ambiguous.vcf             |    7 +
 test/csq/ENST00000624631/ascii-art.txt             |   11 +
 test/csq/ENST00000624631/segfault.txt.new          |    3 +
 test/csq/make-csq-test                             |  276 +
 test/csq/sort-csq                                  |   62 +
 test/fill-tags-hemi.1.out                          |   19 +
 test/fill-tags-hemi.2.out                          |   19 +
 test/{stats.a.vcf => fill-tags-hemi.vcf}           |    9 +-
 test/fill-tags.2.out                               |   27 +-
 test/{fill-tags.2.out => fill-tags.3.out}          |   34 +-
 test/fill-tags.3.smpl                              |    3 +
 test/filter-missing-floats.vcf                     |   42 +
 test/fixref.1.out                                  |   31 +
 test/fixref.vcf                                    |   31 +
 test/guess-ploidy.GL.out                           |    4 +
 test/guess-ploidy.PL.out                           |    4 +
 test/gvcf.merge.1.out                              |   30 +
 test/gvcf.merge.1.vcf                              |   26 +
 test/gvcf.merge.2.vcf                              |   26 +
 test/gvcf.merge.3.vcf                              |   26 +
 test/isec.ab.any.out                               |    2 +
 test/isec.ab.both.out                              |    1 +
 test/large_chrom_tbi_limit.20.1.536870912.out      |    3 -
 test/large_chrom_tbi_limit.vcf                     |   20 -
 test/mendelian.1.out                               |    9 +
 test/mendelian.2.out                               |    8 +
 test/{stats.a.vcf => mendelian.3.out}              |    7 +-
 test/mendelian.vcf                                 |    8 +
 test/merge.2.both.out                              |    4 +-
 test/merge.2.none.out                              |    6 +-
 test/merge.5.a.vcf                                 |    8 +
 test/merge.5.b.vcf                                 |    7 +
 test/merge.5.out                                   |    9 +
 test/{merge.abc.out => merge.abc.2.out}            |   11 +-
 test/{merge.abc.out => merge.abc.3.out}            |   31 +-
 test/merge.abc.out                                 |    9 +-
 test/merge.gvcf.2.a.vcf                            |   33 +
 test/merge.gvcf.2.b.vcf                            |   33 +
 test/merge.gvcf.2.c.vcf                            |   12 +
 test/merge.gvcf.2.out                              |   53 +
 test/mpileup.2.samples                             |    3 +
 test/{mpileup.X.out => mpileup.X.2.out}            |   22 +-
 test/mpileup.X.out                                 |   12 +-
 test/mpileup.c.X.2.out                             |   43 +
 test/mpileup.cAls.out                              |   14 +-
 test/mpileup/mpileup.1.bam                         |  Bin 0 -> 67789 bytes
 test/mpileup/mpileup.1.bam.bai                     |  Bin 0 -> 96 bytes
 test/mpileup/mpileup.1.cram                        |  Bin 0 -> 49113 bytes
 test/mpileup/mpileup.1.cram.crai                   |  Bin 0 -> 42 bytes
 test/mpileup/mpileup.1.out                         |   70 +
 test/mpileup/mpileup.1.sam                         | 1016 ++++
 test/mpileup/mpileup.10.out                        |   70 +
 test/mpileup/mpileup.11.out                        | 4021 ++++++++++++++
 test/mpileup/mpileup.2.bam                         |  Bin 0 -> 27928 bytes
 test/mpileup/mpileup.2.bam.bai                     |  Bin 0 -> 96 bytes
 test/mpileup/mpileup.2.cram                        |  Bin 0 -> 20072 bytes
 test/mpileup/mpileup.2.cram.crai                   |  Bin 0 -> 45 bytes
 test/mpileup/mpileup.2.out                         |  523 ++
 test/mpileup/mpileup.2.sam                         |  248 +
 test/mpileup/mpileup.3.bam                         |  Bin 0 -> 27569 bytes
 test/mpileup/mpileup.3.bam.bai                     |  Bin 0 -> 96 bytes
 test/mpileup/mpileup.3.cram                        |  Bin 0 -> 19643 bytes
 test/mpileup/mpileup.3.cram.crai                   |  Bin 0 -> 43 bytes
 test/mpileup/mpileup.3.out                         |   30 +
 test/mpileup/mpileup.3.sam                         |  250 +
 test/mpileup/mpileup.4.bam                         |  Bin 0 -> 26690 bytes
 test/mpileup/mpileup.4.cram                        |  Bin 0 -> 28165 bytes
 test/mpileup/mpileup.4.out                         |  527 ++
 test/mpileup/mpileup.4.sam                         |  238 +
 test/mpileup/mpileup.5.out                         |  529 ++
 test/mpileup/mpileup.6.out                         |   65 +
 test/mpileup/mpileup.7.out                         |   70 +
 test/mpileup/mpileup.8.out                         |   70 +
 test/mpileup/mpileup.9.out                         |   70 +
 test/mpileup/mpileup.ref.fa                        |   71 +
 test/mpileup/mpileup.ref.fa.fai                    |    1 +
 test/mplp.10.samples                               |    5 +
 test/mplp.11.rgs                                   |    1 +
 test/mplp.9.samples                                |    2 +
 test/mplp.samples                                  |    2 +
 test/norm.out                                      |    1 +
 test/norm.vcf                                      |    2 +
 test/query.24.out                                  |    3 +
 test/query.25.out                                  |   13 +
 test/query.26.out                                  |    1 +
 test/query.27.out                                  |    2 +
 test/query.28.out                                  |    4 +
 test/query.29.out                                  |    3 +
 test/query.30.out                                  |   19 +
 test/query.31.out                                  |   16 +
 test/query.32.out                                  |    3 +
 test/query.33.out                                  |    4 +
 test/query.filter-type.vcf                         |   21 +
 test/query.filter.2.vcf                            |   14 +
 test/ref.out                                       |   30 +
 test/ref.vcf                                       |   30 +
 test/{merge.2.both.out => setGT.1.out}             |   29 +-
 test/{merge.2.both.out => setGT.vcf}               |   29 +-
 test/{stats.chk => stats.B.chk}                    |   46 +-
 test/stats.a.vcf                                   |    1 +
 test/stats.b.vcf                                   |    1 +
 test/stats.chk                                     |   40 +-
 test/test-rbuf.c                                   |    6 +-
 test/test-regidx.c                                 |  374 ++
 test/test.pl                                       |  250 +-
 test/trio.out                                      |    7 +
 test/trio.ped                                      |    6 +
 test/trio.vcf                                      |   16 +
 test/view.GP.vcf                                   |   42 +
 test/view.GT.vcf                                   |   42 +
 test/{fill-tags.2.out => view.GTsubset.NA1.out}    |   23 +-
 test/{fill-tags.2.out => view.GTsubset.NA1NA2.out} |   26 +-
 test/view.GTsubset.NA1NA2NA3.out                   |   36 +
 test/view.vectors.2.vcf                            |   25 +
 test/view.vectors.C.out                            |   28 +
 tsv2vcf.c                                          |    1 +
 vcfannotate.c                                      |  744 +--
 vcfcall.c                                          |   44 +-
 vcfcnv.c                                           |   46 +-
 vcfconcat.c                                        |  164 +-
 vcfconvert.c                                       |  120 +-
 vcffilter.c                                        |    3 +-
 vcfgtcheck.c                                       |  298 +-
 vcfindex.c                                         |  115 +-
 vcfisec.c                                          |    2 +-
 vcfmerge.c                                         | 1075 ++--
 vcfnorm.c                                          |   82 +-
 vcfplugin.c                                        |   56 +-
 vcfroh.c                                           |  961 +++-
 vcfstats.c                                         |  429 +-
 vcfview.c                                          |   50 +-
 484 files changed, 62048 insertions(+), 3674 deletions(-)

-- 
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