[med-svn] samtools branch debian/jessie-backports updated (032962f -> a8be37d)
Afif Elghraoui
afif at moszumanska.debian.org
Sat Aug 6 04:57:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch debian/jessie-backports
in repository samtools.
from 032962f Update GBP configuration for jessie-backport branch.
adds c740a12 Revert "Remove source files not present in upstream tarball"
adds 32bbc45 Fix synopsis and vcs-browser
adds 477fe99 Add lintian-override to document that the language extensions are used internally
adds 8a507bc Fix spelling
adds 9f6248c Mark as team upload since I do not intend to become Uploader for samtools
adds 0777f64 Fix Mayhem issues caused by unlimited reads of gz input
adds 95188c1 Provide some more manpages
adds 663b1a8 Upload to unstable
adds 4a5274b Merge branch 'debian/unstable' of git+ssh://git.debian.org/git/debian-med/samtools into debian/unstable
adds 2e74fb8 Merge version number bump from master
adds f8a6274 Fix typo -- hat tip @mcshane
adds 12c4cba Fixed NM calculation for deletions partially off end of ref.
adds 76870cc Travis builds clone corresponding htslib branch
adds 9c6a5c1 Replace bam_nt16_nt4_table[] by htslib's seq_nt16_int[]
adds f46e5b7 Implement calmd directly against the htslib API
adds 78927b7 Fix calmd -u to write level-0-compressed rather than raw BAM
adds eb21eba Fix @SQ-LN headers to match actual .fa lengths
adds d0c02de Update MD/NM as if by using calmd
adds b7ac1e2 Added error checking around hts_set_fai_filename() calls.
adds 356ca47 Clarify "SAM files differ" error message
adds 918a567 For 0.1.x compatibility, "fixmate - -" writes BAM
adds 8a5a91a Writing SAM files may leave htsExactFormat as text_format
adds 0df9819 Update 00README.txt
adds a83ac9d Add sam_index_load() and samfetch() to legacy API
adds 7dc40b4 [tview] Use iterator directly instead of our own sam_fetch() function
adds e91985a Merge pull request #361 from samtools/samfetch
adds d4f5b07 wgsim: Clarify that -S0 seeds with current time
adds e1714f6 Changed from a local misc/md5.c to using the API in htslib.
adds 329c05f Changes to support the updated htslib md5 interface.
adds 5dfdf2e Rebased and changed to use updated hts_md5_hex.
adds ad9d270 Canonicalise md5sum-lite.c whitespace
adds b542645 Merge use of htslib's MD5 API (PR #354)
adds 016c62b [stats] Implement init_regions(), disabled by missing header API
adds f995b71 [Makefile] Use user's CPPFLAGS/LIBS variables
adds dd76533 samtools dict command to create a sequence dictionary file from a fasta
adds 438e92d Merge new dict command (PR #366)
adds 9f3da06 Handle hts_parse_reg() returning NULL
adds ca44680 [flagstat] Print "N/A" rather than NaN percentages
adds c94d937 stats: make cram index work
adds 84d0702 copy RG, BC and QT tags to the FASTQ header
adds 3f3dbef add bam2fq -t option to man page
adds 33f055c Merge bam2fq RG/BC/QT copying (PR #325)
adds 428b8e2 Make bam_merge_core2 check that sam_index_load() worked.
adds 23bbfd7 Regression.sh fix and mpileup hts_set_fai_filename fix.
adds 738e402 Added -a option to samtools depth.
adds 92899ba Added missing test output files for samtools depth.
adds c03c811 Swapped bam for sam in samtools depth tests.
adds b94f0f2 Added "samtools depth" check outputs to testclean target
adds 15f26e8 Resolved merge conflict
adds 43ca26c Reored usage string
adds f0c42fe Vastly improve performance when many header lines
adds 0736a65 Merge pretty_header() performance improvement (PR #337)
adds 2bf045d Do min_frac comparisons as double rather than float
adds f65869c Extra care for floating point comparisons to avoid 32-bit "make check" failures.
adds 5c3b727 Merge x87 floating point precision workaround
adds 7b5c26c allow samtools merge with one input file
adds 3023e2c added pipe input support to plot-bamstats: use "-" as the bamcheck filename
adds 75ba541 Add samtools 1.0 faidx RAZF->BGZF note
adds e8f27a3 Merge @CO headers
adds b0525f3 Added pointer to our own published zlib benchmarks.
adds 0e19c9e Change --outfile to --output; document faidx warning
adds c2b423c Reduce sam view usage fprintf calls
adds 99f2a2c Further tweak samtools view usage display
adds 7b34693 Merge sam view usage code tweaks (PR #396)
adds 5e6d7bd Update test data for htslib bin corrections
adds 57320c5 Ignore "samtools depth" check outputs
adds 62d7711 Adds 'N' and 'Other' columns to `samtools stats` GCC output. Fixes 376
adds 8b8ed6a Merge 'N' and 'Other' stats columns (PR #397)
adds c18f0f5 plot-bamstats: Remove hard-wired 60 columns fasta lines assumption
adds 23d901e Allow "cmd | samtools view" and write usage to stdout
adds 42098f0 [man page] reorder as per incoming patch [minor]
adds ff95462 Adds missing sections to samtools man page
adds 1fe4b3c Merge man page additions (PR #381)
adds 55c852f Filename to RG ID header fix when merging, fix tab for space in merge tests
adds 44e1a74 Merge filename to RG-ID merge fixes (PR #394)
adds 8a0914e Add checks for bam_hdr_read and sam_hdr_read returning NULL.
adds 5363823 Avoid using asprintf(), which isn't even a POSIX function
adds 9bbc79e Report bam_index_build() errors via stderr and exit status
adds 7802db3 Samtools depad fixes (part 1).
adds 9c2461e Switched to using htslib instead of bam.h. Plus CRAM support.
adds 597b83e Handle CIGAR N in samtools depad by treating as CIGAR D.
adds df5b8e7 Add return value to unpad_seq to allow abort on error
adds f85deba Fixes #201 - thanks Peter.
adds a03575b Merge branch 'develop' into depad
adds e804491 Added depad documentation.
adds 63c060d Further CRAM fixes.
adds 29d6b58 Merge depad improvements and conversion to htslib API (PR #404)
adds 93c45cc Fixed #79
adds 82002e6 Fixed tests.
adds 56a4e74 Fixes segfault in mpileup when alignment is outside of the ref.
adds a717b05 Merge branch 'mpileup-segfault' of https://github.com/Debian/samtools into mpileup_BAQ
adds 39a35af Merge mpileup BAQ fixes (PR #407)
adds a409329 Check ref sequence length before examining ref base
adds eca63aa Without regions, default to 1..INT_MAX rather than 1..2^29
adds 66a9686 Revise stats to handle SECONDARY and SUPPLEMENTARY flagged reads properly
adds 26ddf37 Merge stats supplementary/secondary fixes (PR #357; fixes #352)
adds f845404 Use vcf-miniview to bugfix the broken mpileup BCF test.
adds cd32316 Remove unused warning, update copyright years [minor]
adds c19acd8 Fixes #320 - fixed bug in bam_prob_realn_core with QUAL "*".
adds 66b2f54 Added synonym of -d max_depth to samtools depth for compatibility with mpileup.
adds 41044e3 Describe output format in samtools depth usage string
adds d8fab7a Merge branch 'depth_usage' of https://github.com/peterjc/samtools into develop
adds d968d42 Merge pull request #426 from peterjc/depth_usage
adds 6f8478a Merge branch 'develop' of https://github.com/samtools/samtools into develop
adds 877434b Fixed accidental white space variation.
adds d9ff716 Fixes #328
adds 8f60492 Reactivate "samtools index bam bam.bai" command
adds e2bb18f Add support for multiple file comparison in tests.
adds 227c142 Fix for -c and -p in merge and sort
adds ad1c71e Avoid filenames containing colons, which are invalid on Windows
adds 784b4f5 samtools depth usage typo and longer line wrapping
adds 598f4a0 Replace xz-compressed test data file with gzipped equivalent
adds 04ca943 Enable travis OS X to test cross platform bugs
adds 6d6208a Fixed the mpileup test to avoid floating point 32/64 bit issues.
adds 3b266ba Rewrite samtools reheader in terms of htslib API (instead of bam.h).
adds 160351c Updated samtools reheader to work on CRAM.
adds 1500934 Updates based on pull request comments.
adds 0909586 Merge reheader support for CRAM files (PR #412)
adds 75ae6d4 Merge branch 'develop' of github.com:samtools/samtools into develop
adds 26f57e3 Use POSIX awk gsub() rather than GNU gensub()
adds 1278126 Preserve TAB characters in command to be executed
adds 1669c25 Merge FP last digit removal filter (#445)
adds 999def3 Properly preserve \t and other escape sequences
adds b8ff342 Misc code cleanups
adds 32fd3af Actually test multithreaded Big SAM -> CRAM
adds c404615 Added --output-fmt-option and --input-fmt-option to merge, sort and view.
adds 317e6c9 Added --input-fmt-options arg.
adds 1f577c4 Rationalised the long option handling for "global" options.
adds a515c2c Changed bamshuf to use sam_open instead of bgzf_open so it can handle all formats.
adds 3022021 More --output-fmt-options: fixmate and bamshuf.
adds 14e9a5e Fixed bam split test harness.
adds 942d55f Updated to keep in sync with htslib changes (hts_open_format et al).
adds ff29be9 Fixed bamshuf to use BAM level 1 for temp files and .%s for final output file.
adds dd779ef Fixed use of hts_opt_add following change to htsFormat struct.
adds 4e2cdee Added --input-fmt-option to bam2depth.
adds 367d754 More sub-commands with --input-fmt-option.
adds 723ee29 Fixed bedcov usage. (I'm impressed the test harness spotted this!)
adds 52094e1 Improved usage of CRAM_OPT_REQUIRED_FIELDS.
adds aa7eb08 bam2fq: fixed -O with CRAMs. Also now detects decoding error (BAM or CRAM).
adds b9af7eb More long option handling.
adds ae2332d Fixed an issue causing mpileup --rf and stats --help to fail.
adds af658fb Fixed missing return value in cleanup_state.
adds a63070c Added input/output-fmt-option to man page.
adds d1d3cd2 Minor sam_opts updates
adds c03fec6 Replace assign_short_opts() so struct options can be const
adds 71e1a62 Finish cut_target.c conversion to htslib API
adds b1a5854 Merge --output-fmt-option etc global option handling (PR #395)
adds 8853bc6 Fix FILE* destination for usage output
adds b3fb0f2 Improve man page table formatting [minor]
adds f246dbc Fix stats.c memset() thinko
adds 998188a Adds `samtools quickcheck` subcommand
adds f282777 Add quickcheck subcommand (PR #406)
adds 4054ba5 Reformat main samtools usage display
adds ab561e1 Add accidentally omitted short option [minor]
adds d946f49 Reheader: added explicit version 2.1 and 3.0 cram tests as the code has specific functions for each version.
adds 2877277 Improved test harness to report the errors
adds 3c2003e Merge separate CRAM v2.1 and v3.0 reheader tests
adds 49ed754 Made samtools cat work, when possible, with CRAM files.
adds 8a7a1e7 Fixed samtools cat crash when given invalid filenames.
adds 9f4d361 Added CRAM tests for samtools cat.
adds 7ba7dc3 Use hts_get_format() accessor function
adds 08df3db Merge samtools cat for CRAM files (PR #420, #451)
adds 78c2343 mpileup output updates for VCF4.3
adds 4bf1886 resolve merge conflict
adds 5edde1e skip first bin for AD and DPR calculations as this stores the totals for the site
adds 0c5617e Merge mpileup updates for VCF v4.3 (PR #448)
adds e55418f Prefix errors with "samtools <subcmd>:" rather than "samtools:"
adds 9f0a46f Amend SAM header merge strategy to avoid two quadratic-cost operations and switch from expensive regexes to simple string.h operations.
adds a181403 Merge branch 'develop' of https://github.com/samtools/samtools into header_merge_efficiency
adds 5812c9b Add facility to escape regex inputs
adds 9951654 Merge pull request samtools#436 into branch for samtools#419
adds 4dda617 Make test_trans_tbl_init build and run successfully.
adds 858b0e7 Improve header merging.
adds 7190607 Replace regex searches with dedicated match function.
adds 226cb15 Deal with out of order @SQ lines.
adds dce3c28 Merge header merge non-regex-based rewrite (PR #453)
adds ddcde25 allow to set the fraction of ambiguous bases
adds 86b0b1e bugfix: missing inserted allele in output
adds 9ab4379 output contiguous deletion
adds e72b245 Fixed wgsim bugs.
adds 8be7f04 Merge James's wgsim bug fixes
adds 8e3e23f Add manpage for wgsim
adds d779e25 Merged wgsim_eval.pl with https://github.com/lh3/wgsim/commits/master/wgsim_eval.pl
adds 4bfd611 Added some help to wgsim alneval.
adds 8e9b6f9 Tidied up white space to be consistent across entire file.
adds 7e4b541 Support for X and = in CIGAR strings
adds ea5a92f Merge misc/wgsim updates and man page (PR #428)
adds 7584cf6 Allow splitting of statistics on tags
adds 09cf53c Use stats_t* over intptr_t in hash
adds df82d58 Rename hash to c2stats to reflect previous intptr->stat_t* [minor]
adds 881e224 Rename split option -T/--tag-split to -S/--split
adds dbea849 Merge samtools stats splitting (PR #421)
adds 1849a6e Fixed wgsim so that it doesn't have infinite loops if it finds a sequence of Ns.
adds 3c0e3a5 Add stats split prefix support and split indicator
adds 8f3e729 Have stats --split-prefix set the output prefix rather than adding to it
adds 3e9357c Merge stats split output filename prefix (PR #460)
adds 5b3280d Document make targets to build htslib utilities
adds 2bd7837 Update stats --split-prefix usage to match 8f3e729
adds 4d2efe9 Use kstring's kgetline()
adds 8d792d2 Inverse video mode for tview and also changed some colours.
adds fcaafe0 Merge pull request #459 from samtools/tview_colours
adds 495b86c Add missing Makefile dependencies
adds 093192e Canonicalise Makefile dependencies [minor]
adds f75eb34 Calmd now accpets the global I/O options.
adds 8123d02 Minimal fix to make --reference replace -f fasta_ref when not explicitly specified.
adds 5520372 Tview now uses --reference value if specified (and ref not manually specified)
adds 77761c3 Added depad to help output.
adds cf18e41 Added global i/o options to "samtools depad".
adds 3ab5f6c Made targetcut -f and --reference the same option.
adds 13de48f Added a bam_get_library() implementation.
adds fff21fe Updated the rmdup command to use the newer htslib interface instead of the old bam.h one.
adds 77c8b4e Added recently changed #include dependencies to Makefile.
adds 25bee0e Added calls to sam_open_mode() to auto-detect file format by name.
adds 11ccd2a Added -o/-U filename.<suffix> detection to samtools view.
adds af76b1a Reformat calmd_usage() to 2-space option indentation
adds caea801 Merge --output-fmt-option etc followup (PR #461)
adds e0306d2 Port addreplacerg command over from separate repo
adds 0bd5498 Add ability to add new RG to file.
adds 74b4c59 Add long input and output format options to addreplacerg
adds 9a8f2f6 Fixes for addrprg based on @jmarshall's review
adds 798c7bc Correct stated default mode for addreplacerg
adds 9397387 addreplacerg style fixes, usage correction and bugfix
adds 17a8d79 Fix addrprg entertaining off by one error, spec valid but breaks stuff
adds 7c4cce4 Add addreplacerg command (PR #371)
adds dffc67f Added code to fix #343, thanks @cyrusmaher for the pointer in the right direction
adds 56c9437 Fix typo in conditional [minor]
adds f0cb72c Split out bam1_t to fastq processing and add option to output to files.
adds 289ae95 Comments to explain bam2fq mainloop
adds 20b5b13 Refactor bam2fq arg parsing and init
adds e762eec Add comments to bam2fq mainloop
adds 6353367 samtools bam2qf option to force FASTA or FASTQ output
adds 76300af Set default FASTQ quality with samtools bam2fq -v INT
adds 50ad1b5 Rewrite branch 'bam2fq_format' of github.com:peterjc/samtools into bam2fq_improve
adds b73d36e Rewrite of bam2fq singleton tracking with tests
adds 6a22b4f Rename bam2fq to fastq and fasta respectively
adds 3978eca Fixup bam2fq true and false, update copyright dates and man page.
adds f44f54d Miscellaneous tidy-ups [minor]
adds 834bf7e Merge bam2fq improvements (PR #263)
adds e066deb Make merge allow input files with no @HD line
adds 6e4bc52 Merge pull request #476 from daviesrob/merge_no_hd
adds 87cdc4a Define and use .EX/.EE macros for examples and code blocks
adds f78373c `samtools sort` usage [Fixes #418,#356,#349,#295]
adds 370c7ea Merge develop's --output-fmt-option changes in bam_sort()
adds 7f2bc8e Update legacy-attempt heuristics and diagnostics
adds d637d59 Avoid memory leaks on invocation error abends
adds a997205 Merge legacy sort usage removal (PR #441)
adds 4040496 Document "*" region query for unmapped read pairs
adds 3af0bec Describe $HTS_PATH, the search path for HTSlib plugins
adds f2c357c Reformat merge usage
adds fe1868b Update merge -cp usage
adds 4d56437 Improve error messages for opening or format errors
adds 97c9883 Rename bamshuf to collate
adds 90dcd90 Allow for n_targets==0 in finish_merged_header() shrinking
adds 803143b Made --threads long option versions of - at .
adds defd753 Use $(htslib_kfoo_h) make variables for htslib/k* headers
adds ea6d10c Add configure.ac script
adds 3c15c88 Always link with -rdynamic/-ldl [hack]
adds 4b4e688 Update INSTALL etc to discuss configuring samtools
adds ed3191b Samtools release 1.3: many improvements, bug fixes, and new commands
adds 95c561d Merge tag '1.3' into debian/unstable
adds 824f68f New upstream release; no new copyright nor license notice.
adds 86a9375 Replace LDLIBS by LIBS, following upstream changelog.
adds c12f4f3 Removed patch; issue solved upstream.
adds 5c4ca0b Removed patch; issue solved upstream.
adds 4988ce7 adapt to new build system
adds 45397bc use secure Vcs-Git
adds f1e3f7c patch configure.in to not call make in m4_esyscmd_s()
adds 6479cce add Build-Dep to automake
adds 487e759 cleanup copyright
adds d985799 add patch header
adds 82f34d3 patch spelling
adds 9d12a17 update d/changelog
adds a9bf06a add NEWS for 1.3 commandline API changes
adds 096bc41 dch -r
adds 493b1ca Merge version number bump and NEWS file from master
adds 3c197df set a matrix.include for all os options
adds befba2e Include <unistd.h> for isatty() [minor]
adds de68be6 Happy New Year
adds 664cc5f Fixed a known-failure (mpileup -d) issue; now passes.
adds 74a3e0a Add #include <config.h> to all *.c source files [minor]
adds 59ab663 Fix -O option for reads without OQ tag
adds 03a6bc5 Improved documentation of mpileup -l vs -r.
adds a5cdff6 Remove gcc build on OSX
adds c613147 Tidied up the mpileup.[123].sam files to not use RNAME fields with no @SQ records.
adds 23b91e8 Improved documentation of how mpileup -d/-L work.
adds c152c47 Fix typo.
adds 3d792ba Merge pull request #525 from samtools/mpileup_depth
adds bf85440 Grammar fix.
adds dae373b Ignore .exe extension; don't force core and ~ ignorance
adds ac5b8e7 Use AC_SYS_LARGEFILE configure test instead of -D_FILE_OFFSET_BITS=64
adds ce44eb3 Add check on hts_close to quickcheck
adds 6e3ac27 Fixed bam_get_library() crash.
adds 2dcdd62 Adds a usage note to `samtools quickcheck`
adds d49c73b Reformat "Notes" in long -? usage output
adds 3c8a69f Fix samtools merge -n usage doc [minor]
adds f63a282 Recreate missing @SQ header from BAM binary header
adds cd7e005 Fix indentation [minor]
adds 3baa47b manpage: fix typo [minor]
adds 09dda53 fastx: only show relevant usage options for fasta/fastq commands
adds 3312225 Merge fasta usage message improvements (PR #555)
adds 6994f30 Check sam_read1() return value correctly
adds de96bfb Fix warnings from adding HTS_RESULT_USED to htslib prototypes.
adds 0e260d9 Ensure fp is always closed in write_buffer.
adds 24d3235 Use print_error_errno() where appropriate
adds 1152881 Various tidying up and segfault fixes
adds f6db782 Merge error checking improvements (PR #467)
adds 72679e1 Fix \r\n thinko [minor]
adds 9968e4c Make samtools sort notice when it clobbers other sorts
adds 5f53e3c Propagate errno from sort worker threads
adds b5047ab Removed a (harmless) perl warning from test harness.
adds 8471a0d Add `@CO` headers only once when merging sort temp files
adds 5839af6 Write sort's temporary files alongside the *output* file
adds 897c002 Samtools release 1.3.1: bug fixes, notably sort temporary file fixes
adds 0c961b2 Merge tag '1.3.1' into debian/unstable
adds 0de58f7 New upstream release; no new copyright nor license notice.
adds 3666b08 Conforms with Policy version 3.9.8.
adds 82c3bfa Remove legacy statement on the libbam.
adds 60c45b7 samtools (1.3.1-1) unstable; urgency=medium
adds 952da10 Needs htslib 1.3.1.
adds 0296398 Current changelog.
adds a98b89b samtools (1.3.1-2) unstable; urgency=medium
new 84ee7a1 Merge tag 'debian/1.3.1-2' into debian/jessie-backports
new a8be37d releasing package samtools version 1.3.1-2~bpo8+1
The 2 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 | 2 +-
.gitignore | 14 +-
.travis.yml | 22 +-
.travis/clone | 14 +
INSTALL | 144 +-
Makefile | 242 +-
NEWS | 145 +-
README | 31 +-
README.md | 25 +
bam.c | 85 +-
bam.h | 14 +-
bam2bcf.c | 77 +-
bam2bcf.h | 13 +-
bam2bcf_indel.c | 16 +-
bam2depth.c | 144 +-
bam_addrprg.c | 478 ++
bam_aux.c | 20 +-
bam_cat.c | 501 +-
bam_color.c | 2 +
bam_flags.c | 2 +
bam_import.c | 2 +
bam_index.c | 31 +-
bam_lpileup.c | 2 +
bam_mate.c | 134 +-
bam_md.c | 217 +-
bam_plbuf.c | 2 +
bam_plcmd.c | 238 +-
bam_quickcheck.c | 154 +
bam_reheader.c | 485 +-
bam_rmdup.c | 173 +-
bam_rmdupse.c | 79 +-
bam_sort.c | 1651 ++--
bam_split.c | 165 +-
bam_stat.c | 68 +-
bam_tview.c | 90 +-
bam_tview.h | 6 +-
bam_tview_curses.c | 112 +-
bam_tview_html.c | 12 +-
bamshuf.c | 229 +-
bamtk.c | 113 +-
bedcov.c | 33 +-
bedidx.c | 2 +
config.h.in | 50 +
config.mk.in | 52 +
configure.ac | 103 +
cut_target.c | 72 +-
debian/NEWS | 9 +
debian/README.Debian | 9 -
debian/ax_with_htslib.m4 | 140 +
debian/changelog | 49 +
debian/control | 17 +-
debian/copyright | 24 +-
debian/mans/ace2sam.1 | 24 +
debian/mans/samtools.pl.1 | 19 +
debian/mans/wgsim.1 | 44 +
debian/patches/fix_segfault_with_small_ref.patch | 54 -
debian/patches/i386-build.patch | 48 -
debian/patches/literal_version.patch | 16 +
debian/patches/mayhem.patch | 69 +
debian/patches/series | 6 +-
debian/patches/spelling.patch | 15 +
debian/rules | 21 +-
debian/samtools.install | 1 +
debian/samtools.lintian-overrides | 4 +
debian/source/options | 1 +
dict.c | 154 +
errmod.c | 6 +-
examples/00README.txt | 2 +-
faidx.c | 6 +-
install-sh | 501 ++
kprobaln.c | 2 +
misc/ace2sam.c | 2 +
misc/maq2sam.c | 2 +
misc/md5.c | 298 -
misc/md5.h | 57 -
misc/md5fa.c | 49 +-
bam_plbuf.c => misc/md5sum-lite.c | 69 +-
misc/plot-bamstats | 25 +-
misc/wgsim.1 | 55 +
misc/wgsim.c | 145 +-
misc/wgsim_eval.pl | 376 +-
padding.c | 319 +-
phase.c | 119 +-
sam.c | 45 +-
sam.h | 26 +-
sam_header.c | 2 +
sam_opts.c | 155 +
sam_opts.h | 99 +
sam_view.c | 809 +-
sample.c | 2 +
samtools.1 | 1500 +++-
samtools.h | 12 +-
stats.c | 1077 +--
stats_isize.c | 2 +
test/addrprg/1_fixup.sam | 30 +
test/addrprg/1_fixup.sam.expected | 30 +
.../1_fixup.sam.expected.err} | 0
test/addrprg/2_fixup_orphan.sam | 30 +
test/addrprg/2_fixup_orphan.sam.expected | 30 +
.../2_fixup_orphan.sam.expected.err} | 0
.../3_fixup.sam.expected} | 0
test/addrprg/3_fixup.sam.expected.err | 1 +
test/addrprg/4_fixup_norg.sam | 29 +
test/addrprg/4_fixup_norg.sam.expected | 30 +
.../4_fixup_norg.sam.expected.err} | 0
test/bam2fq/1.1.fq.expected | 72 +
test/bam2fq/1.2.fq.expected | 72 +
.../empty.expected => bam2fq/1.stdout.expected} | 0
test/bam2fq/2.1.fq.expected | 72 +
test/bam2fq/2.2.fq.expected | 72 +
.../{dat/empty.expected => bam2fq/2.s.fq.expected} | 0
.../empty.expected => bam2fq/2.stdout.expected} | 0
test/bam2fq/3.1.fq.expected | 72 +
test/bam2fq/3.2.fq.expected | 72 +
test/bam2fq/3.s.fq.expected | 4 +
.../empty.expected => bam2fq/3.stdout.expected} | 0
test/bam2fq/4.1.fq.expected | 68 +
test/bam2fq/4.2.fq.expected | 68 +
test/bam2fq/4.s.fq.expected | 8 +
.../empty.expected => bam2fq/4.stdout.expected} | 0
test/dat/.gitignore | 2 +
test/dat/bam2fq.001.sam | 9 +-
test/dat/{bam2fq.001.sam => bam2fq.002.sam} | 10 +-
test/dat/{bam2fq.001.sam => bam2fq.003.sam} | 11 +-
test/dat/depad.001p.sam | 12 +-
test/dat/depad.001u.sam | 14 +-
test/dat/dict.fa | 46 +
test/dat/dict.out | 10 +
test/dat/mpileup.1.sam | 44 +-
test/dat/mpileup.2.sam | 10 +-
test/dat/mpileup.3.sam | 14 +-
test/dat/mpileup.out.2 | 1006 +--
test/dat/mpileup.out.4 | 1008 +--
test/dat/test_input_1_a.bam | Bin 758 -> 759 bytes
...1_a.bam.bai => test_input_1_a.bam.bai.expected} | Bin
test/dat/test_input_1_a_regex.sam | 28 +
test/dat/test_input_1_b.bam | Bin 687 -> 686 bytes
test/dat/test_input_1_b.bam.bai | Bin 192 -> 0 bytes
test/dat/test_input_1_b.sam | 2 +-
test/dat/test_input_1_b_regex.sam | 24 +
test/dat/test_input_1_c.bam | Bin 655 -> 692 bytes
test/dat/test_input_1_c.bam.bai | Bin 176 -> 0 bytes
test/dat/test_input_1_c.sam | 1 +
test/dat/view.001.sam | 2 +-
test/merge/.gitignore | 1 -
test/merge/2.merge.expected.bam | Bin 1181 -> 1228 bytes
test/merge/3.merge.expected.bam | Bin 1199 -> 1233 bytes
test/merge/3.merge.expected.err | 6 +-
test/merge/4.merge.expected.bam | Bin 0 -> 689 bytes
test/merge/5.merge.expected.bam | Bin 0 -> 1115 bytes
test/merge/5.merge.expected.sam | 61 +
test/merge/6.merge.expected.bam | Bin 0 -> 899 bytes
test/merge/7.merge.expected.bam | Bin 0 -> 1056 bytes
test/merge/test_bam_translate.c | 37 +-
test/merge/test_pretty_header.c | 87 -
test/merge/test_rtrans_build.c | 2 +
test/merge/test_trans_tbl_init.c | 417 +-
test/mpileup/.gitignore | 1 +
test/mpileup/depth.reg | 39 +
test/mpileup/expected/1.out.f3-6.gz | Bin 0 -> 596114 bytes
test/mpileup/expected/1.out.xz | Bin 1336220 -> 0 bytes
test/mpileup/expected/11.out | 18 +-
test/mpileup/expected/12.out | 18 +-
test/mpileup/expected/16.out | 182 +-
test/mpileup/expected/19.out | 182 +-
test/mpileup/expected/20.out | 12 +-
test/mpileup/expected/21.out | 182 +-
test/mpileup/expected/22.out | 182 +-
test/mpileup/expected/23.out | 4 +-
test/mpileup/expected/24.out | 4 +-
test/mpileup/expected/25.out | 4 +-
test/mpileup/expected/33.out | 4 +-
test/mpileup/expected/34.out | 4 +-
test/mpileup/expected/4.out | 56 +-
test/mpileup/expected/48.out | 8202 ++++++++++----------
test/mpileup/expected/49.out | 8202 ++++++++++----------
test/mpileup/expected/50.out | 8202 ++++++++++----------
test/mpileup/expected/51.out | 8202 ++++++++++----------
test/mpileup/expected/52.out | 4209 +++++++++-
test/mpileup/expected/76.out | 182 +-
test/mpileup/expected/77.out | 182 +-
test/mpileup/expected/d1_1.out | 6 +
test/mpileup/expected/d1_12.out | 9 +
test/mpileup/expected/d1_2.out | 6 +
test/mpileup/expected/d2_12r.out | 5 +
test/mpileup/expected/d3_12.out | 20 +
test/mpileup/expected/d3_12r1a.out | 12 +
test/mpileup/expected/d3_12r2a.out | 6 +
test/mpileup/expected/d4_12.out | 60 +
test/mpileup/expected/d4_12b.out | 17 +
test/mpileup/expected/d4_12r.out | 12 +
test/mpileup/mpileup.reg | 8 +-
test/mpileup/regression.sh | 18 +-
test/mpileup/xx#depth1.sam | 6 +
test/mpileup/xx#depth2.sam | 6 +
test/mpileup/xx.bed | 2 +
test/mpileup/xx.bed2 | 1 +
test/quickcheck/1.quickcheck.badeof.bam | Bin 0 -> 1228 bytes
test/quickcheck/2.quickcheck.badheader.bam | Bin 0 -> 1233 bytes
test/quickcheck/3.quickcheck.ok.bam | Bin 0 -> 1228 bytes
test/quickcheck/4.quickcheck.ok.bam | Bin 0 -> 1233 bytes
test/quickcheck/5.quickcheck.truncated.cram | Bin 0 -> 11960 bytes
test/quickcheck/all.expected | 3 +
.../view.001.sam => reheader/1_view1.sam.expected} | 11 +-
.../1_view1.sam.expected.err} | 0
.../2_view1.sam.expected} | 61 +-
.../2_view1.sam.expected.err} | 0
.../3_view1.sam.expected} | 57 +-
.../3_view1.sam.expected.err} | 0
test/{dat/cat.hdr => reheader/hdr.sam} | 7 +-
test/split/test_count_rg.c | 11 +-
test/split/test_expand_format_string.c | 15 +-
test/split/test_filter_header_rg.c | 17 +-
test/split/test_parse_args.c | 34 +-
test/stat/1.stats.expected | 72 +-
test/stat/{5.stats.expected => 10.stats.expected} | 250 +-
test/stat/{1_map_cigar.sam => 10_map_cigar.sam} | 3 +
...ed => 10_map_cigar.sam_s1_a_1.expected.bamstat} | 72 +-
...ed => 10_map_cigar.sam_s1_b_1.expected.bamstat} | 72 +-
...ted => 1_map_cigar.sam_s1_a_1.expected.bamstat} | 72 +-
test/stat/2.stats.expected | 72 +-
test/stat/3.stats.expected | 2 +-
test/stat/4.stats.expected | 72 +-
test/stat/5.stats.expected | 72 +-
test/stat/6.stats.expected | 72 +-
test/stat/{5.stats.expected => 7.stats.expected} | 83 +-
test/stat/7_supp.sam | 6 +
test/stat/{5.stats.expected => 8.stats.expected} | 76 +-
test/stat/{5_insert_cigar.sam => 8_secondary.sam} | 1 +
test/stat/{1.stats.expected => 9.stats.expected} | 72 +-
test/test.c | 2 +
test/test.pl | 282 +-
test/tview/test_get_rg_sample.c | 2 +
test/vcf-miniview.c | 2 +
234 files changed, 34197 insertions(+), 22219 deletions(-)
create mode 100755 .travis/clone
create mode 100644 bam_addrprg.c
create mode 100644 bam_quickcheck.c
create mode 100644 config.h.in
create mode 100644 config.mk.in
create mode 100644 configure.ac
create mode 100644 debian/NEWS
create mode 100644 debian/ax_with_htslib.m4
create mode 100644 debian/mans/ace2sam.1
create mode 100644 debian/mans/samtools.pl.1
create mode 100644 debian/mans/wgsim.1
delete mode 100644 debian/patches/fix_segfault_with_small_ref.patch
delete mode 100644 debian/patches/i386-build.patch
create mode 100644 debian/patches/literal_version.patch
create mode 100644 debian/patches/mayhem.patch
create mode 100644 debian/patches/spelling.patch
create mode 100644 debian/samtools.lintian-overrides
create mode 100644 dict.c
create mode 100755 install-sh
delete mode 100644 misc/md5.c
delete mode 100644 misc/md5.h
copy bam_plbuf.c => misc/md5sum-lite.c (53%)
create mode 100644 misc/wgsim.1
create mode 100644 sam_opts.c
create mode 100644 sam_opts.h
create mode 100644 test/addrprg/1_fixup.sam
create mode 100644 test/addrprg/1_fixup.sam.expected
copy test/{dat/empty.expected => addrprg/1_fixup.sam.expected.err} (100%)
create mode 100644 test/addrprg/2_fixup_orphan.sam
create mode 100644 test/addrprg/2_fixup_orphan.sam.expected
copy test/{dat/empty.expected => addrprg/2_fixup_orphan.sam.expected.err} (100%)
copy test/{dat/empty.expected => addrprg/3_fixup.sam.expected} (100%)
create mode 100644 test/addrprg/3_fixup.sam.expected.err
create mode 100644 test/addrprg/4_fixup_norg.sam
create mode 100644 test/addrprg/4_fixup_norg.sam.expected
copy test/{dat/empty.expected => addrprg/4_fixup_norg.sam.expected.err} (100%)
create mode 100644 test/bam2fq/1.1.fq.expected
create mode 100644 test/bam2fq/1.2.fq.expected
copy test/{dat/empty.expected => bam2fq/1.stdout.expected} (100%)
create mode 100644 test/bam2fq/2.1.fq.expected
create mode 100644 test/bam2fq/2.2.fq.expected
copy test/{dat/empty.expected => bam2fq/2.s.fq.expected} (100%)
copy test/{dat/empty.expected => bam2fq/2.stdout.expected} (100%)
create mode 100644 test/bam2fq/3.1.fq.expected
create mode 100644 test/bam2fq/3.2.fq.expected
create mode 100644 test/bam2fq/3.s.fq.expected
copy test/{dat/empty.expected => bam2fq/3.stdout.expected} (100%)
create mode 100644 test/bam2fq/4.1.fq.expected
create mode 100644 test/bam2fq/4.2.fq.expected
create mode 100644 test/bam2fq/4.s.fq.expected
copy test/{dat/empty.expected => bam2fq/4.stdout.expected} (100%)
create mode 100644 test/dat/.gitignore
copy test/dat/{bam2fq.001.sam => bam2fq.002.sam} (90%)
copy test/dat/{bam2fq.001.sam => bam2fq.003.sam} (90%)
create mode 100644 test/dat/dict.fa
create mode 100644 test/dat/dict.out
rename test/dat/{test_input_1_a.bam.bai => test_input_1_a.bam.bai.expected} (100%)
create mode 100644 test/dat/test_input_1_a_regex.sam
delete mode 100644 test/dat/test_input_1_b.bam.bai
create mode 100644 test/dat/test_input_1_b_regex.sam
delete mode 100644 test/dat/test_input_1_c.bam.bai
create mode 100644 test/merge/4.merge.expected.bam
create mode 100644 test/merge/5.merge.expected.bam
create mode 100644 test/merge/5.merge.expected.sam
create mode 100644 test/merge/6.merge.expected.bam
create mode 100644 test/merge/7.merge.expected.bam
delete mode 100644 test/merge/test_pretty_header.c
create mode 100644 test/mpileup/depth.reg
create mode 100644 test/mpileup/expected/1.out.f3-6.gz
delete mode 100644 test/mpileup/expected/1.out.xz
create mode 100644 test/mpileup/expected/d1_1.out
create mode 100644 test/mpileup/expected/d1_12.out
create mode 100644 test/mpileup/expected/d1_2.out
create mode 100644 test/mpileup/expected/d2_12r.out
create mode 100644 test/mpileup/expected/d3_12.out
create mode 100644 test/mpileup/expected/d3_12r1a.out
create mode 100644 test/mpileup/expected/d3_12r2a.out
create mode 100644 test/mpileup/expected/d4_12.out
create mode 100644 test/mpileup/expected/d4_12b.out
create mode 100644 test/mpileup/expected/d4_12r.out
create mode 100644 test/mpileup/xx#depth1.sam
create mode 100644 test/mpileup/xx#depth2.sam
create mode 100644 test/mpileup/xx.bed
create mode 100644 test/mpileup/xx.bed2
create mode 100644 test/quickcheck/1.quickcheck.badeof.bam
create mode 100644 test/quickcheck/2.quickcheck.badheader.bam
create mode 100644 test/quickcheck/3.quickcheck.ok.bam
create mode 100644 test/quickcheck/4.quickcheck.ok.bam
create mode 100644 test/quickcheck/5.quickcheck.truncated.cram
create mode 100644 test/quickcheck/all.expected
copy test/{dat/view.001.sam => reheader/1_view1.sam.expected} (95%)
copy test/{dat/empty.expected => reheader/1_view1.sam.expected.err} (100%)
copy test/{dat/bam2fq.001.sam => reheader/2_view1.sam.expected} (62%)
copy test/{dat/empty.expected => reheader/2_view1.sam.expected.err} (100%)
copy test/{dat/bam2fq.001.sam => reheader/3_view1.sam.expected} (62%)
copy test/{dat/empty.expected => reheader/3_view1.sam.expected.err} (100%)
copy test/{dat/cat.hdr => reheader/hdr.sam} (83%)
copy test/stat/{5.stats.expected => 10.stats.expected} (95%)
copy test/stat/{1_map_cigar.sam => 10_map_cigar.sam} (53%)
copy test/stat/{1.stats.expected => 10_map_cigar.sam_s1_a_1.expected.bamstat} (97%)
copy test/stat/{1.stats.expected => 10_map_cigar.sam_s1_b_1.expected.bamstat} (97%)
copy test/stat/{1.stats.expected => 1_map_cigar.sam_s1_a_1.expected.bamstat} (97%)
copy test/stat/{5.stats.expected => 7.stats.expected} (97%)
create mode 100644 test/stat/7_supp.sam
copy test/stat/{5.stats.expected => 8.stats.expected} (97%)
copy test/stat/{5_insert_cigar.sam => 8_secondary.sam} (71%)
copy test/stat/{1.stats.expected => 9.stats.expected} (97%)
--
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