[med-svn] samtools branch master updated (255f97d -> ed3191b)
Charles Plessy
plessy at moszumanska.debian.org
Thu Dec 24 05:00:33 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository samtools.
from 255f97d Release 1.2: various bug fixes
new 2e74fb8 Merge version number bump from master
new f8a6274 Fix typo -- hat tip @mcshane
new 12c4cba Fixed NM calculation for deletions partially off end of ref.
new 76870cc Travis builds clone corresponding htslib branch
new 9c6a5c1 Replace bam_nt16_nt4_table[] by htslib's seq_nt16_int[]
new f46e5b7 Implement calmd directly against the htslib API
new 78927b7 Fix calmd -u to write level-0-compressed rather than raw BAM
new eb21eba Fix @SQ-LN headers to match actual .fa lengths
new d0c02de Update MD/NM as if by using calmd
new b7ac1e2 Added error checking around hts_set_fai_filename() calls.
new 356ca47 Clarify "SAM files differ" error message
new 918a567 For 0.1.x compatibility, "fixmate - -" writes BAM
new 8a5a91a Writing SAM files may leave htsExactFormat as text_format
new 0df9819 Update 00README.txt
new a83ac9d Add sam_index_load() and samfetch() to legacy API
new 7dc40b4 [tview] Use iterator directly instead of our own sam_fetch() function
new e91985a Merge pull request #361 from samtools/samfetch
new d4f5b07 wgsim: Clarify that -S0 seeds with current time
new e1714f6 Changed from a local misc/md5.c to using the API in htslib.
new 329c05f Changes to support the updated htslib md5 interface.
new 5dfdf2e Rebased and changed to use updated hts_md5_hex.
new ad9d270 Canonicalise md5sum-lite.c whitespace
new b542645 Merge use of htslib's MD5 API (PR #354)
new 016c62b [stats] Implement init_regions(), disabled by missing header API
new f995b71 [Makefile] Use user's CPPFLAGS/LIBS variables
new dd76533 samtools dict command to create a sequence dictionary file from a fasta
new 438e92d Merge new dict command (PR #366)
new 9f3da06 Handle hts_parse_reg() returning NULL
new ca44680 [flagstat] Print "N/A" rather than NaN percentages
new c94d937 stats: make cram index work
new 84d0702 copy RG, BC and QT tags to the FASTQ header
new 3f3dbef add bam2fq -t option to man page
new 33f055c Merge bam2fq RG/BC/QT copying (PR #325)
new 428b8e2 Make bam_merge_core2 check that sam_index_load() worked.
new 23bbfd7 Regression.sh fix and mpileup hts_set_fai_filename fix.
new 738e402 Added -a option to samtools depth.
new 92899ba Added missing test output files for samtools depth.
new c03c811 Swapped bam for sam in samtools depth tests.
new b94f0f2 Added "samtools depth" check outputs to testclean target
new 15f26e8 Resolved merge conflict
new 43ca26c Reored usage string
new f0c42fe Vastly improve performance when many header lines
new 0736a65 Merge pretty_header() performance improvement (PR #337)
new 2bf045d Do min_frac comparisons as double rather than float
new f65869c Extra care for floating point comparisons to avoid 32-bit "make check" failures.
new 5c3b727 Merge x87 floating point precision workaround
new 7b5c26c allow samtools merge with one input file
new 3023e2c added pipe input support to plot-bamstats: use "-" as the bamcheck filename
new 75ba541 Add samtools 1.0 faidx RAZF->BGZF note
new e8f27a3 Merge @CO headers
new b0525f3 Added pointer to our own published zlib benchmarks.
new 0e19c9e Change --outfile to --output; document faidx warning
new c2b423c Reduce sam view usage fprintf calls
new 99f2a2c Further tweak samtools view usage display
new 7b34693 Merge sam view usage code tweaks (PR #396)
new 5e6d7bd Update test data for htslib bin corrections
new 57320c5 Ignore "samtools depth" check outputs
new 62d7711 Adds 'N' and 'Other' columns to `samtools stats` GCC output. Fixes 376
new 8b8ed6a Merge 'N' and 'Other' stats columns (PR #397)
new c18f0f5 plot-bamstats: Remove hard-wired 60 columns fasta lines assumption
new 23d901e Allow "cmd | samtools view" and write usage to stdout
new 42098f0 [man page] reorder as per incoming patch [minor]
new ff95462 Adds missing sections to samtools man page
new 1fe4b3c Merge man page additions (PR #381)
new 55c852f Filename to RG ID header fix when merging, fix tab for space in merge tests
new 44e1a74 Merge filename to RG-ID merge fixes (PR #394)
new 8a0914e Add checks for bam_hdr_read and sam_hdr_read returning NULL.
new 5363823 Avoid using asprintf(), which isn't even a POSIX function
new 9bbc79e Report bam_index_build() errors via stderr and exit status
new 7802db3 Samtools depad fixes (part 1).
new 9c2461e Switched to using htslib instead of bam.h. Plus CRAM support.
new 597b83e Handle CIGAR N in samtools depad by treating as CIGAR D.
new df5b8e7 Add return value to unpad_seq to allow abort on error
new f85deba Fixes #201 - thanks Peter.
new a03575b Merge branch 'develop' into depad
new e804491 Added depad documentation.
new 63c060d Further CRAM fixes.
new 29d6b58 Merge depad improvements and conversion to htslib API (PR #404)
new 93c45cc Fixed #79
new 82002e6 Fixed tests.
adds 56a4e74 Fixes segfault in mpileup when alignment is outside of the ref.
new a717b05 Merge branch 'mpileup-segfault' of https://github.com/Debian/samtools into mpileup_BAQ
new 39a35af Merge mpileup BAQ fixes (PR #407)
new a409329 Check ref sequence length before examining ref base
new eca63aa Without regions, default to 1..INT_MAX rather than 1..2^29
new 66a9686 Revise stats to handle SECONDARY and SUPPLEMENTARY flagged reads properly
new 26ddf37 Merge stats supplementary/secondary fixes (PR #357; fixes #352)
new f845404 Use vcf-miniview to bugfix the broken mpileup BCF test.
new cd32316 Remove unused warning, update copyright years [minor]
new c19acd8 Fixes #320 - fixed bug in bam_prob_realn_core with QUAL "*".
new 66b2f54 Added synonym of -d max_depth to samtools depth for compatibility with mpileup.
new 41044e3 Describe output format in samtools depth usage string
new d8fab7a Merge branch 'depth_usage' of https://github.com/peterjc/samtools into develop
new d968d42 Merge pull request #426 from peterjc/depth_usage
new 6f8478a Merge branch 'develop' of https://github.com/samtools/samtools into develop
new 877434b Fixed accidental white space variation.
new d9ff716 Fixes #328
new 8f60492 Reactivate "samtools index bam bam.bai" command
new e2bb18f Add support for multiple file comparison in tests.
new 227c142 Fix for -c and -p in merge and sort
new ad1c71e Avoid filenames containing colons, which are invalid on Windows
new 784b4f5 samtools depth usage typo and longer line wrapping
new 598f4a0 Replace xz-compressed test data file with gzipped equivalent
new 04ca943 Enable travis OS X to test cross platform bugs
new 6d6208a Fixed the mpileup test to avoid floating point 32/64 bit issues.
new 3b266ba Rewrite samtools reheader in terms of htslib API (instead of bam.h).
new 160351c Updated samtools reheader to work on CRAM.
new 1500934 Updates based on pull request comments.
new 0909586 Merge reheader support for CRAM files (PR #412)
new 75ae6d4 Merge branch 'develop' of github.com:samtools/samtools into develop
new 26f57e3 Use POSIX awk gsub() rather than GNU gensub()
new 1278126 Preserve TAB characters in command to be executed
new 1669c25 Merge FP last digit removal filter (#445)
new 999def3 Properly preserve \t and other escape sequences
new b8ff342 Misc code cleanups
new 32fd3af Actually test multithreaded Big SAM -> CRAM
new c404615 Added --output-fmt-option and --input-fmt-option to merge, sort and view.
new 317e6c9 Added --input-fmt-options arg.
new 1f577c4 Rationalised the long option handling for "global" options.
new a515c2c Changed bamshuf to use sam_open instead of bgzf_open so it can handle all formats.
new 3022021 More --output-fmt-options: fixmate and bamshuf.
new 14e9a5e Fixed bam split test harness.
new 942d55f Updated to keep in sync with htslib changes (hts_open_format et al).
new ff29be9 Fixed bamshuf to use BAM level 1 for temp files and .%s for final output file.
new dd779ef Fixed use of hts_opt_add following change to htsFormat struct.
new 4e2cdee Added --input-fmt-option to bam2depth.
new 367d754 More sub-commands with --input-fmt-option.
new 723ee29 Fixed bedcov usage. (I'm impressed the test harness spotted this!)
new 52094e1 Improved usage of CRAM_OPT_REQUIRED_FIELDS.
new aa7eb08 bam2fq: fixed -O with CRAMs. Also now detects decoding error (BAM or CRAM).
new b9af7eb More long option handling.
new ae2332d Fixed an issue causing mpileup --rf and stats --help to fail.
new af658fb Fixed missing return value in cleanup_state.
new a63070c Added input/output-fmt-option to man page.
new d1d3cd2 Minor sam_opts updates
new c03fec6 Replace assign_short_opts() so struct options can be const
new 71e1a62 Finish cut_target.c conversion to htslib API
new b1a5854 Merge --output-fmt-option etc global option handling (PR #395)
new 8853bc6 Fix FILE* destination for usage output
new b3fb0f2 Improve man page table formatting [minor]
new f246dbc Fix stats.c memset() thinko
new 998188a Adds `samtools quickcheck` subcommand
new f282777 Add quickcheck subcommand (PR #406)
new 4054ba5 Reformat main samtools usage display
new ab561e1 Add accidentally omitted short option [minor]
new d946f49 Reheader: added explicit version 2.1 and 3.0 cram tests as the code has specific functions for each version.
new 2877277 Improved test harness to report the errors
new 3c2003e Merge separate CRAM v2.1 and v3.0 reheader tests
new 49ed754 Made samtools cat work, when possible, with CRAM files.
new 8a7a1e7 Fixed samtools cat crash when given invalid filenames.
new 9f4d361 Added CRAM tests for samtools cat.
new 7ba7dc3 Use hts_get_format() accessor function
new 08df3db Merge samtools cat for CRAM files (PR #420, #451)
new 78c2343 mpileup output updates for VCF4.3
new 4bf1886 resolve merge conflict
new 5edde1e skip first bin for AD and DPR calculations as this stores the totals for the site
new 0c5617e Merge mpileup updates for VCF v4.3 (PR #448)
new e55418f Prefix errors with "samtools <subcmd>:" rather than "samtools:"
new 9f0a46f Amend SAM header merge strategy to avoid two quadratic-cost operations and switch from expensive regexes to simple string.h operations.
new a181403 Merge branch 'develop' of https://github.com/samtools/samtools into header_merge_efficiency
new 5812c9b Add facility to escape regex inputs
new 9951654 Merge pull request samtools#436 into branch for samtools#419
new 4dda617 Make test_trans_tbl_init build and run successfully.
new 858b0e7 Improve header merging.
new 7190607 Replace regex searches with dedicated match function.
new 226cb15 Deal with out of order @SQ lines.
new dce3c28 Merge header merge non-regex-based rewrite (PR #453)
new ddcde25 allow to set the fraction of ambiguous bases
new 86b0b1e bugfix: missing inserted allele in output
new 9ab4379 output contiguous deletion
new e72b245 Fixed wgsim bugs.
new 8be7f04 Merge James's wgsim bug fixes
new 8e3e23f Add manpage for wgsim
new d779e25 Merged wgsim_eval.pl with https://github.com/lh3/wgsim/commits/master/wgsim_eval.pl
new 4bfd611 Added some help to wgsim alneval.
new 8e9b6f9 Tidied up white space to be consistent across entire file.
new 7e4b541 Support for X and = in CIGAR strings
new ea5a92f Merge misc/wgsim updates and man page (PR #428)
new 7584cf6 Allow splitting of statistics on tags
new 09cf53c Use stats_t* over intptr_t in hash
new df82d58 Rename hash to c2stats to reflect previous intptr->stat_t* [minor]
new 881e224 Rename split option -T/--tag-split to -S/--split
new dbea849 Merge samtools stats splitting (PR #421)
new 1849a6e Fixed wgsim so that it doesn't have infinite loops if it finds a sequence of Ns.
new 3c0e3a5 Add stats split prefix support and split indicator
new 8f3e729 Have stats --split-prefix set the output prefix rather than adding to it
new 3e9357c Merge stats split output filename prefix (PR #460)
new 5b3280d Document make targets to build htslib utilities
new 2bd7837 Update stats --split-prefix usage to match 8f3e729
new 4d2efe9 Use kstring's kgetline()
new 8d792d2 Inverse video mode for tview and also changed some colours.
new fcaafe0 Merge pull request #459 from samtools/tview_colours
new 495b86c Add missing Makefile dependencies
new 093192e Canonicalise Makefile dependencies [minor]
new f75eb34 Calmd now accpets the global I/O options.
new 8123d02 Minimal fix to make --reference replace -f fasta_ref when not explicitly specified.
new 5520372 Tview now uses --reference value if specified (and ref not manually specified)
new 77761c3 Added depad to help output.
new cf18e41 Added global i/o options to "samtools depad".
new 3ab5f6c Made targetcut -f and --reference the same option.
new 13de48f Added a bam_get_library() implementation.
new fff21fe Updated the rmdup command to use the newer htslib interface instead of the old bam.h one.
new 77c8b4e Added recently changed #include dependencies to Makefile.
new 25bee0e Added calls to sam_open_mode() to auto-detect file format by name.
new 11ccd2a Added -o/-U filename.<suffix> detection to samtools view.
new af76b1a Reformat calmd_usage() to 2-space option indentation
new caea801 Merge --output-fmt-option etc followup (PR #461)
new e0306d2 Port addreplacerg command over from separate repo
new 0bd5498 Add ability to add new RG to file.
new 74b4c59 Add long input and output format options to addreplacerg
new 9a8f2f6 Fixes for addrprg based on @jmarshall's review
new 798c7bc Correct stated default mode for addreplacerg
new 9397387 addreplacerg style fixes, usage correction and bugfix
new 17a8d79 Fix addrprg entertaining off by one error, spec valid but breaks stuff
new 7c4cce4 Add addreplacerg command (PR #371)
new dffc67f Added code to fix #343, thanks @cyrusmaher for the pointer in the right direction
new 56c9437 Fix typo in conditional [minor]
new f0cb72c Split out bam1_t to fastq processing and add option to output to files.
new 289ae95 Comments to explain bam2fq mainloop
new 20b5b13 Refactor bam2fq arg parsing and init
new e762eec Add comments to bam2fq mainloop
new 6353367 samtools bam2qf option to force FASTA or FASTQ output
new 76300af Set default FASTQ quality with samtools bam2fq -v INT
new 50ad1b5 Rewrite branch 'bam2fq_format' of github.com:peterjc/samtools into bam2fq_improve
new b73d36e Rewrite of bam2fq singleton tracking with tests
new 6a22b4f Rename bam2fq to fastq and fasta respectively
new 3978eca Fixup bam2fq true and false, update copyright dates and man page.
new f44f54d Miscellaneous tidy-ups [minor]
new 834bf7e Merge bam2fq improvements (PR #263)
new e066deb Make merge allow input files with no @HD line
new 6e4bc52 Merge pull request #476 from daviesrob/merge_no_hd
new 87cdc4a Define and use .EX/.EE macros for examples and code blocks
new f78373c `samtools sort` usage [Fixes #418,#356,#349,#295]
new 370c7ea Merge develop's --output-fmt-option changes in bam_sort()
new 7f2bc8e Update legacy-attempt heuristics and diagnostics
new d637d59 Avoid memory leaks on invocation error abends
new a997205 Merge legacy sort usage removal (PR #441)
new 4040496 Document "*" region query for unmapped read pairs
new 3af0bec Describe $HTS_PATH, the search path for HTSlib plugins
new f2c357c Reformat merge usage
new fe1868b Update merge -cp usage
new 4d56437 Improve error messages for opening or format errors
new 97c9883 Rename bamshuf to collate
new 90dcd90 Allow for n_targets==0 in finish_merged_header() shrinking
new 803143b Made --threads long option versions of - at .
new defd753 Use $(htslib_kfoo_h) make variables for htslib/k* headers
new ea6d10c Add configure.ac script
new 3c15c88 Always link with -rdynamic/-ldl [hack]
new 4b4e688 Update INSTALL etc to discuss configuring samtools
new ed3191b Samtools release 1.3: many improvements, bug fixes, and new commands
The 249 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 | 9 +
.travis.yml | 14 +-
.travis/clone | 14 +
INSTALL | 144 +-
Makefile | 212 +-
NEWS | 104 +-
README | 31 +-
README.md | 25 +
bam.c | 67 +-
bam.h | 7 +-
bam2bcf.c | 75 +-
bam2bcf.h | 13 +-
bam2bcf_indel.c | 14 +-
bam2depth.c | 142 +-
bam_addrprg.c | 476 ++
bam_aux.c | 18 +-
bam_cat.c | 432 +-
bam_index.c | 29 +-
bam_mate.c | 58 +-
bam_md.c | 173 +-
bam_plcmd.c | 232 +-
bam_quickcheck.c | 134 +
bam_reheader.c | 437 +-
bam_rmdup.c | 94 +-
bam_rmdupse.c | 31 +-
bam_sort.c | 1472 +++-
bam_split.c | 99 +-
bam_stat.c | 66 +-
bam_tview.c | 88 +-
bam_tview.h | 6 +-
bam_tview_curses.c | 112 +-
bam_tview_html.c | 10 +-
bamshuf.c | 112 +-
bamtk.c | 107 +-
bedcov.c | 31 +-
config.h.in | 39 +
config.mk.in | 52 +
configure.ac | 101 +
cut_target.c | 70 +-
dict.c | 151 +
errmod.c | 4 +-
examples/00README.txt | 2 +-
install-sh | 501 ++
misc/md5.c | 298 -
misc/md5.h | 57 -
misc/md5fa.c | 47 +-
bam_plbuf.c => misc/md5sum-lite.c | 67 +-
misc/plot-bamstats | 25 +-
misc/wgsim.1 | 55 +
misc/wgsim.c | 143 +-
misc/wgsim_eval.pl | 376 +-
padding.c | 287 +-
phase.c | 44 +-
sam.c | 29 +-
sam.h | 26 +-
sam_opts.c | 153 +
sam_opts.h | 99 +
sam_view.c | 795 +-
samtools.1 | 1458 +++-
samtools.h | 12 +-
stats.c | 1075 +--
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 | 2 +-
test/dat/mpileup.2.sam | 2 +-
test/dat/mpileup.3.sam | 2 +-
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/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 | 35 +-
test/merge/test_pretty_header.c | 87 -
test/merge/test_trans_tbl_init.c | 415 +-
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 | 6 +-
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/all.expected | 2 +
.../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 | 9 +-
test/split/test_expand_format_string.c | 13 +-
test/split/test_filter_header_rg.c | 15 +-
test/split/test_parse_args.c | 32 +-
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.pl | 270 +-
196 files changed, 32785 insertions(+), 21836 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 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 (54%)
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/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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