[med-svn] samtools branch debian/unstable updated (0bc88ca -> 7e76eb3)
Andreas Tille
tille at debian.org
Tue Mar 21 18:17:31 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch debian/unstable
in repository samtools.
from 0bc88ca Remove wrong debian-changes patch
new 7d3f3a8 Merge version number bump and NEWS file from master
new 9627ffb HTSlib now provides errmod_cal() etc
new a60dd37 Use HTSlib's new sam_prob_realn() and sam_cap_mapq() functions
new f846d65 Use HTSlib's new probaln_glocal() function
new 4f9a327 Use HTSlib's new errmod_cal()/probaln_glocal()/sam_prob_realn() functions
new 9e4093d Explicitly set @CURSES_LIB@ for --without-curses
new 026c8d7 Write BQ SAM line the same way as for AF
new e4446b5 Use bcf_hdr_format() rather than deprecated bcf_hdr_fmt_text()
new e5dfb0a Add samtools view tests for extracting unmapped reads.
new 1c1c219 Fixed the out by one error in --insert-size.
new b4e452c Added mpileup -a and -aa options
new 69567c8 bam2fq_mainloop should be using filter_it_out
new 4db01dd Improved error reporting in samtools index.
new 4dbadcf Enforce a minimum memory requirement for samtools sort
new b2b81b4 Merge sort memory requirement diagnostic (PR #581)
new 4f8adc8 Add NEWS item about mpileup zero coverage '*' fixes
new d0c09f3 Convert quickcheck to hts_check_EOF API to check EOF on CRAM
new 1395f12 Fix Rob and Martin's whitespace [minor]
new 402aa76 Fixed the `-a` option for zero coverage positions
new 44290dd Depth/Mpileup -a fixes. Fixes #374.
new 9c5fd98 Added 30ish new tests for depth/mpileup -a and -aa.
new 675bff7 Merge mpileup/depth -a/-aa fixes (PR #579, PR #586)
new 2fa144f Further depth/mpileup tests. Also improved documentation.
new f458b7c Testclean and ignore test temporary files
new 39c4b67 Amend info regarding bedcov subcommand
new cbea0f9 Allow finer control over program vs. script installation
new 73c4054 Add libst.a so test suite can use print_error()/etc
new 29cfd70 Use print_error/_errno() in bam_sort.c and bam_split.c
new a04a7dd Avoid printing "error message: Success" [minor]
new 324d662 bam_split now adds @PG header to bam files (PR #557)
new f3178b7 Avoid strndup() and strsep() for portability reasons
new 91283dd In read_file_list(), check for URL syntax or extant files
new b25695b Add plot-bamstats -l / --log-y option
new 26e1ea5 Clarify bedcov subcommand usage
new de10fa3 Make samtools faidx write faster and detect write errors.
new 613501f Exterminate error(), fix memory leaks in event of write errors
new d1039b9 Fix language misidentification of test data [minor]
new 9df6321 Use print_error_errno() to report file open failures
new a9054c7 Place percent mapped bases output in the correct field
new 04ce2bc Improve view -s documentation
new ce4a601 Skip usage tests when pseudo-terminal can't be opened
new 0a15035 Fix usage description of bamshuf/collate
new 4b8bdd4 Happy New Year
new 1bae251 Listen to -o FILE option in samtools view -c
new 30bc5e2 Add the autoconf macros required to the repository
new 28a611d Added multi-threaded decoding to view, index and sort.
new 24971ad Improved multi-threading support for many more samtools commands.
new 002eb0a Remove redundant item from long options array
new 3a7d0f0 Update some tests to run both single and multi-threaded
new d02c177 Temporarily disable the large_chrom bai index test
new 2e84f7b Add MC support to fixmates
new 9adfa13 Add error handling to kstring functions in bam_mate
new e5f5ba1 Fixmates: add tests for two reads unmapped
new c39caa4 Replaced bool with int to avoid confusion with true being failure.
new 80ed7c7 Merged PR#545 (Add MC support to fixmates)
new 6c4929d Fix to 28a611d2 to prevent samtools view crash on error handling.
new 90b0baa index: update error message for failure to index
new cbee45e Fixed a typo: changed "suffices" to "suffixes".
new 5ec72f1 Mention multi-threaded BAM/CRAM decoding.
new 6587a2b Use htslib_static.mk to get static link flags
new 979bac9 Merge branch PR #649 (Use htslib_static.mk to get static link flags)
new 1bf9afa Updated with 1.4 changes
new c63b06e Add liblzma and libbz2 to travis.
new 3f0407f Stop samtools configure from always trying to configure htslib
new e5838c2 Update INSTALL with new library dependencies
new 0a859b1 Release 1.4: summary
new bda1d8a Merge tag '1.4' into debian/unstable
new f83cd5e Replaced Dominique Belhachemi by my own ID as Uploader
new 0dafb69 Adapt patches
new 7e76eb3 Bump versioned Depends: libhts-dev (>= 1.4), upload to experimental
The 70 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:
.gitattributes | 3 +
.travis.yml | 12 +
INSTALL | 37 +-
Makefile | 110 +-
NEWS | 40 +-
README | 6 +-
README.md | 12 +-
bam.h | 2 +-
bam2bcf.c | 2 +-
bam2bcf.h | 2 +-
bam2bcf_indel.c | 12 +-
bam2depth.c | 30 +-
bam_addrprg.c | 86 +-
bam_index.c | 52 +-
bam_mate.c | 71 +-
bam_md.c | 202 +-
bam_plcmd.c | 121 +-
bam_quickcheck.c | 52 +-
bam_rmdup.c | 4 +-
bam_sort.c | 125 +-
bam_split.c | 99 +-
bam_stat.c | 28 +-
bam_tview.c | 13 +-
bamshuf.c | 22 +-
bamtk.c | 35 +-
bedcov.c | 8 +-
config.mk.in | 6 +-
configure.ac | 8 +
cut_target.c | 19 +-
debian/changelog | 10 +-
debian/control | 4 +-
debian/patches/fix-test.patch | 23 -
debian/patches/series | 1 -
errmod.c | 194 -
errmod.h | 49 -
faidx.c | 74 +-
kprobaln.c | 282 -
kprobaln.h | 49 -
{debian => m4}/ax_with_curses.m4 | 112 +-
{debian => m4}/ax_with_htslib.m4 | 24 +-
misc/ace2sam.c | 5 +-
misc/plot-bamstats | 11 +-
misc/wgsim.1 | 2 +-
padding.c | 4 +-
phase.c | 6 +-
sam_opts.c | 8 +-
sam_opts.h | 7 +-
samtools.h => sam_utils.c | 57 +-
sam_view.c | 67 +-
samtools.1 | 58 +-
stats.c | 18 +-
test/dat/view.001.fa | 2 +
test/dat/view.001.fa.fai | 1 +
test/dat/view.001.sam | 1 +
test/fixmate/1_coord_sort.sam | 2 +
test/fixmate/2_isize_overflow.sam | 2 +
test/fixmate/2_isize_overflow.sam.expected | 14 +-
test/fixmate/3_reverse_read_pp_lt.sam.expected | 4 +-
test/fixmate/4_reverse_read_pp_equal.sam.expected | 4 +-
test/fixmate/5_ct.sam.expected | 4 +-
test/fixmate/6_ct_replace.sam.expected | 4 +-
...{2_isize_overflow.sam => 7_two_read_mapped.sam} | 6 +-
...sam.expected => 7_two_read_mapped.sam.expected} | 18 +-
test/mpileup/.gitignore | 2 +-
test/mpileup/depth.reg | 49 +
test/mpileup/expected/14.out | 32 +-
test/mpileup/expected/15.out | 32 +-
test/mpileup/expected/16.out | 34 +-
test/mpileup/expected/19.out | 34 +-
test/mpileup/expected/20.out | 6796 ++++++++++----------
test/mpileup/expected/21.out | 34 +-
test/mpileup/expected/22.out | 34 +-
test/mpileup/expected/23.out | 2 +-
test/mpileup/expected/24.out | 2 +-
test/mpileup/expected/25.out | 2 +-
test/mpileup/expected/30.out | 2 +-
test/mpileup/expected/32.out | 2 +-
test/mpileup/expected/34.out | 4 +-
test/mpileup/expected/35.out | 60 +-
test/mpileup/expected/43.out | 4 +-
test/mpileup/expected/44.out | 4 +-
test/mpileup/expected/6.out | 2 +-
test/mpileup/expected/7.out | 2 +-
test/mpileup/expected/a0.out | 4200 ++++++++++++
test/mpileup/expected/a1.out | 20 +
test/mpileup/expected/a10.out | 6 +
test/mpileup/expected/a11.out | 6 +
test/mpileup/expected/a13.out | 12 +
test/mpileup/expected/a14.out | 17 +
test/mpileup/expected/a15.out | 20 +
test/mpileup/expected/a16.out | 20 +
test/mpileup/expected/a17.out | 20 +
test/mpileup/expected/a2.out | 20 +
test/mpileup/expected/a3.out | 20 +
test/mpileup/expected/a4.out | 60 +
test/mpileup/expected/a5.out | 60 +
test/mpileup/expected/a6.out | 60 +
test/mpileup/expected/a8.out | 12 +
test/mpileup/expected/a9.out | 12 +
test/mpileup/expected/d3_3.out | 40 +
test/mpileup/expected/d5_all1.out | 6 +
test/mpileup/expected/d5_all2.out | 40 +
test/mpileup/expected/d5_all3.out | 80 +
test/mpileup/expected/d5_b3.out | 3 +
test/mpileup/expected/d5_b3a.out | 7 +
test/mpileup/expected/d5_b3aa.out | 14 +
.../expected/d5_blank.out} | 0
test/mpileup/expected/d5_xx1.out | 3 +
test/mpileup/expected/d5_xx2.out | 7 +
test/mpileup/expected/d5_xx3.out | 12 +
test/mpileup/expected/d5_xy1.out | 2 +
test/mpileup/expected/m5_all1.out | 6 +
test/mpileup/expected/m5_all2.out | 40 +
test/mpileup/expected/m5_all3.out | 80 +
test/mpileup/expected/m5_b3.out | 3 +
test/mpileup/expected/m5_b3a.out | 7 +
test/mpileup/expected/m5_b3aa.out | 14 +
.../expected/m5_blank.out} | 0
test/mpileup/expected/m5_xx1.out | 3 +
test/mpileup/expected/m5_xx2.out | 7 +
test/mpileup/expected/m5_xx3.out | 12 +
test/mpileup/expected/m5_xy1.out | 2 +
test/mpileup/mpileup.reg | 54 +-
test/mpileup/{xx#depth1.sam => xx#depth3.sam} | 3 +-
test/mpileup/xx.bed3 | 3 +
test/mpileup/xx.fa | 1 -
...cram => 5.quickcheck.scramble30.truncated.cram} | Bin
test/quickcheck/6.quickcheck.cram21.ok.cram | Bin 0 -> 154443 bytes
test/quickcheck/7.quickcheck.cram30.ok.cram | Bin 0 -> 49122 bytes
test/quickcheck/8.quickcheck.cram21.truncated.cram | Bin 0 -> 154413 bytes
test/quickcheck/9.quickcheck.cram30.truncated.cram | Bin 0 -> 49084 bytes
test/quickcheck/all.expected | 4 +-
test/split/test_filter_header_rg.c | 15 +-
test/test.c | 8 +-
test/test.pl | 126 +-
test/vcf-miniview.c | 12 +-
136 files changed, 9708 insertions(+), 4950 deletions(-)
delete mode 100644 debian/patches/fix-test.patch
delete mode 100644 errmod.c
delete mode 100644 errmod.h
delete mode 100644 kprobaln.c
delete mode 100644 kprobaln.h
copy {debian => m4}/ax_with_curses.m4 (86%)
copy {debian => m4}/ax_with_htslib.m4 (83%)
copy samtools.h => sam_utils.c (54%)
copy test/fixmate/{2_isize_overflow.sam => 7_two_read_mapped.sam} (82%)
copy test/fixmate/{2_isize_overflow.sam.expected => 7_two_read_mapped.sam.expected} (60%)
create mode 100644 test/mpileup/expected/a0.out
create mode 100644 test/mpileup/expected/a1.out
create mode 100644 test/mpileup/expected/a10.out
create mode 100644 test/mpileup/expected/a11.out
create mode 100644 test/mpileup/expected/a13.out
create mode 100644 test/mpileup/expected/a14.out
create mode 100644 test/mpileup/expected/a15.out
create mode 100644 test/mpileup/expected/a16.out
create mode 100644 test/mpileup/expected/a17.out
create mode 100644 test/mpileup/expected/a2.out
create mode 100644 test/mpileup/expected/a3.out
create mode 100644 test/mpileup/expected/a4.out
create mode 100644 test/mpileup/expected/a5.out
create mode 100644 test/mpileup/expected/a6.out
create mode 100644 test/mpileup/expected/a8.out
create mode 100644 test/mpileup/expected/a9.out
create mode 100644 test/mpileup/expected/d3_3.out
create mode 100644 test/mpileup/expected/d5_all1.out
create mode 100644 test/mpileup/expected/d5_all2.out
create mode 100644 test/mpileup/expected/d5_all3.out
create mode 100644 test/mpileup/expected/d5_b3.out
create mode 100644 test/mpileup/expected/d5_b3a.out
create mode 100644 test/mpileup/expected/d5_b3aa.out
copy test/{addrprg/1_fixup.sam.expected.err => mpileup/expected/d5_blank.out} (100%)
create mode 100644 test/mpileup/expected/d5_xx1.out
create mode 100644 test/mpileup/expected/d5_xx2.out
create mode 100644 test/mpileup/expected/d5_xx3.out
create mode 100644 test/mpileup/expected/d5_xy1.out
create mode 100644 test/mpileup/expected/m5_all1.out
create mode 100644 test/mpileup/expected/m5_all2.out
create mode 100644 test/mpileup/expected/m5_all3.out
create mode 100644 test/mpileup/expected/m5_b3.out
create mode 100644 test/mpileup/expected/m5_b3a.out
create mode 100644 test/mpileup/expected/m5_b3aa.out
copy test/{addrprg/1_fixup.sam.expected.err => mpileup/expected/m5_blank.out} (100%)
create mode 100644 test/mpileup/expected/m5_xx1.out
create mode 100644 test/mpileup/expected/m5_xx2.out
create mode 100644 test/mpileup/expected/m5_xx3.out
create mode 100644 test/mpileup/expected/m5_xy1.out
copy test/mpileup/{xx#depth1.sam => xx#depth3.sam} (72%)
create mode 100644 test/mpileup/xx.bed3
rename test/quickcheck/{5.quickcheck.truncated.cram => 5.quickcheck.scramble30.truncated.cram} (100%)
create mode 100644 test/quickcheck/6.quickcheck.cram21.ok.cram
create mode 100644 test/quickcheck/7.quickcheck.cram30.ok.cram
create mode 100644 test/quickcheck/8.quickcheck.cram21.truncated.cram
create mode 100644 test/quickcheck/9.quickcheck.cram30.truncated.cram
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