[med-svn] samtools branch debian/unstable updated (05b622e -> 89a7c0e)
Charles Plessy
plessy at moszumanska.debian.org
Mon Aug 18 01:39:48 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository samtools.
from 05b622e Move debian/upstream to debian/upstream/metadata
new 63336cc Don't set text-is-cached flag if reading headers encountered EOF
new 5fe45f3 Raise error if give @HD SO:coordinate to 'samtools fixmate'
new fcdecf1 Merge pull request #20, fixmate aborts on SO:coordinate
new bd5f0a0 Fix buffer overflow
new 0bea4a7 Remove double fclose()
new b53e632 Silence -Wstrict-prototypes warnings in main header files
new 431a5e9 Catch overflow in n_cigar and give an explicit error.
new bacb46c Merge cigar length check (PR #39)
new 037bdb1 Fix control of compression level in bam_merge_core2
new 63a54ff Set Git attributes similarly to the develop branch
new 48b4b70 Release 0.1.20: final non-htslib standalone samtools
new 69f08ea mpileup: Removed bcf_hdr_fmt_text() which is no longer necessary
new 2bd2417 Implement view & bam2fq directly against the htslib API
new dd48869 Updated test
new 63f8590 flags: Fixed a typo
new 839a16d mpileup: -q now takes effect also with -C
new 66797d8 mpileup: Apply -Q switch also to MQ output
new aa410be samtools flags: add documentation. print out decimal representation in addition to hexadecimal and string representation
new 1b408f7 Merge pull request #121 from sm15/feature/bam_flags_docs
new 660da5b Use new sam_itr_*() htslib API for BAM/CRAM iterators
new e2d7559 [bedcov] Use the htslib API directly, now works with BAM or CRAM files
new cbff696 Use htslib's bam_endpos() instead of copied old bam_calend() code
new ce958a2 Fix typos in the manpage.
new 4c09100 Merge pull request #118, fixing man page typos
new f2abc5e fixed spelling mistake
new 4f8660e Merge pull request #141 from sb10/develop
new ce1efc6 Replace bam2fq numbers with existing constants
new 66507a7 Remove global variables from samtools view
new 296d029 Add ability to strip aux tags to samtools view
new f3a306f Merge pull request #109 from aux_tag_strip of github.com/mp15/samtools
new 41bcf93 Add properly paired to stats and correct definition in flagstat
new dc6df77 Merge pull request #106, properly-paired flag statistics
new c82cbad Shut up, clang!
new df763f3 mpileup: Fixed broken IMF annotation
new 55bb89e Added mpileup tests for CRAM
new c643abc Make int size explicit for bcf_get_*_int calls
new d85db72 Add some more comments to tview
new b3376c4 Reenable tview and port to htslib
new 917c3e1 Restore sample selection to tview and add a unit test for the code doing it.
new 0b5be10 Use htslib facilities instead of bam_parse_region()
new 54eaa39 Revert unnecessary changes on tview branch
new a985c51 Fix tview-related dependencies
new dd030b2 Merge pull request #93, convert tview to htslib API
new 088b9d2 Use sam_itr_*()/etc, enabling tview on CRAM files
new a8398f9 Fix "Usage: ..." message
new 93dbf71 Added links to 'sister' projects.
new 058b94f Merge #148, links to 'sister' projects (but omitting ourself)
new 26bb0c4 stats: More understandable output fields naming
new e3328b4 Updated mpileup test to reflect change in overlap quals
new cbcbe48 Add a few comments to bam merging function
new 29dcd07 WIP on header merging
new 94eaa16 Add target id translation code and write pseudo code for building RG and PG translation tables
new 6e03078 Convert PG and RG pseudo code to working code. Add pseudocode for PG PP: translation. Add -D_GNU_SOURCE for some of the newer POSIX functions
new 3b2b9a5 Further work on bam merge to fix header produced
new 2033785 Fix bugs picked up by unit testing. Make trans_tbl_t a named struct and move aside variable names the same as it.
new 796fc4a More work on merging @RG and @PG tags into header.
new 933445d Unit tests for merge
new 9dfc2df add skeleton code for PP processing
new 2ab1f3d NULLify some freed pointers. Add tracing statement
new 6ea18e8 Unit test trans_tbl_init add test 5 for PG tags
new 1a50bcc Fix memory leaks and finalise @PG PP handling
new b3c4002 Test @PG merging and PP handling
new 71ec46e Integrate new header merging code into bam_sort main function
new dc65fbe Clean up old dead code
new 7fdda46 Fix case where PG or RG tag is present on read but not in header. Fix translation of tid == -1 aka unmapped. Sort out extra \n in header text.
new 63f7a33 Add test bams
new 97797cc Fix spaces to tabs
new c007fa0 Eliminate compiler warnings in a cross-platform safe way. Tweak comments a bit.
new 3ff2373 Add unit test for bam_translate (WIP)
new 988d565 Fix edge case
new bcc1d24 Add unit test for tid translation
new 7548729 Add additional unit tests for bam_translate for PG and RG tags.
new 64cb9fd Adjust how merge handles duplicated PG and RG tags.
new 6f494ec Add command line support for combining tags
new c2667f5 Don't merge header into itself
new b4f86f6 Correct header length in test
new c5c128f Fix memory leak in trans_tbl_init Comment on MERGE_force
new b73ff8e Enhance description of what we do
new 563fcb6 Add warning when merging causes coordinate sort to be lost
new 6abb25b Reorder merge code so that BAM gets translated before it is inserted into heap. Create reverse translation table for merge region selection. Define memset_pattern4 for non-OS X systems.
new dde3359 Create slightly more sophisticated unit tests for merge
new 38c6408 Convert merge reverse translation build to own function.
new a936181 Ensure make only runs on make test Trap stderr in unit bam_translate test. Restructure bam_translate unit test for new format.
new 06c849d Add clock based randomness to merge and option to fix random seed.
new e4af837 Correct lost sort order detection in merge
new 1f910e5 Fix regex to pick out sequence ids
new edeacbb Add rtrans_build unit test stub
new c8c818f More work on rtrans_build unit test. Update test makefile to include rtrans_build test. Add additional sam test file for merge to exercise missing target @SQ, especially in region merge.
new 7a31715 Fix position of bam_translate in merge read loop.
new 702b1f6 Deal with case where merged region does not exist in header of one of our input files. Update merge to htslib indexes.
new 20f2b62 hts_iter_t is not a pointer unlike it's predecessor
new f0e05f4 Add function to prettify header output by sorting it by defined order.
new 85ee78d Instead of relying on NULL iter in merge use HTS_IDX_START
new 45965ae Ignore generated test files Add additional test sam to test case where targets differ
new 44b63f1 In bam sort and merge change: * pointer == 0 to == NULL * pointer = 0 to = NULL
new 7c77832 Fix merge unit tests under Linux
new a202dbe Initialise un-inited variable in test_bam_translate.
new 1ffd06d Revise merge header matching regex from spec
new 159f0cb Make it easier to tell merge test phases apart
new a18dde7 Apparently some programs put spaces into their @PG and @RG ID's.
new cf43d54 Add option to vary level of verbosity. Truncate file between tests. Correct test 6 for bam_translate.
new d4d4867 Fix bug where wrong flag was being checked in header merge (merge rg vs merge pg) Add @RG PG tag rewriting, this all needs cleaning up and consolidating now.
new 4c4da26 Add PG tags to @RG lines testcases.
new 4e9bcf9 When merging instead of segfaulting when there is no index, return an error. Need to think of better ways to handle this.
new 3dff60d Fix to use htslib commands.
new e6ed9ca Port bam_sort.c completely to new API.
new 275283a Fix up tests for htslib architecture
new 46ca8f1 Add -b option to merge to allow the specification of a list of files as alternative to putting them on the command line.
new 3ef90e9 Fix control of compression level in bam_merge_core. The setting was ineffective due to a minor copy/paste error.
new 413af26 Use sam_itr_*()/etc and enable compiling with current htslib
new 452dd14 Update dependencies and define _GNU_SOURCE only for bam_sort.o
new 3181d5f Use htslib facilities instead of bam_parse_region() etc
new 742b501 Make I/O redirection portable (to Linux)
new 9838b1b Add test/merge/* test programs to main Makefile
new 229e0ae Merge pull request #70, merge improvements
new 8657d9a Limits -Q option (qual_scale) to sensible range 0 to 93.
new 147afae bam_merge: get rid of asprintf warnings
new b63021f bam_merge tests: fix warnings
new feab370 Create xfreopen() utility instead of duplicating code
new 04eeec5 Use kstring instead of asprintf()
new 22247f1 Merge asprintf()->kstring rewrite and warning fixes (#161)
new 3f92248 Fix buffer overflow
new 7a87169 Use kstring instead of strndup()
new ab05e1e Makes -r and -R read group filtering options both use settings.rghash
new 73a00ad Ensures non-zero exit if -r / -R options fail to work.
new 5fab219 Extant code in sam_view.c does not use Yoda conditions
new c17f353 Merge read group filtering changes (PR #164)
new 72cd75e Convert samtools stats to htslib
new 07c0a23 Add Test files for stats
new 80b25ca Merge pull request #174 from mp15/stats
new 8054f37 Print dummy column for MAPQ for mpileup -s
new fcc64e9 Disconnect clean-htslib from clean target
new bfb0376 Fix compiler warning in stats
new d23efe0 Enable tests for samtools stats
new aeb923a Merge pull request #179 from mp15/stats
new f189079 Rewrite bed_read
new 91be501 Adds check to ensure bed_read worked, and exits non-zero if not.
new 610db9c Stops samtools view from writing unmapped reads with -L (BED file) option
new a5fabc5 Don't malloc the kstring_t; minor changes to the big comment
new 11414ac Merge BED file parsing improvements (PR #165)
new 99d13d8 add -U FILE to output unselected reads for pipelin
new 6460586 Merge view -U option (PR #177), also adding it to the man page
new 16c73e7 Makes samtools view subsampling option more random.
new ea92f59 Merge view subsampling randomness (PR #167, fixes #160)
new 06acafc Adds *~ (emacs backup files) and core to .gitignore.
new e859892 Adds tests for samtools view.
new 7b845e9 Merge branch 'develop' into develop_testing
new c468057 Turns on CRAM region tests, now that CRAM indexing is supported.
new c382302 Adds -L (BED file reading) tests.
new 59171a3 Adds tests for the -t, -T and -B options.
new f03d590 Adds more region tests.
new abe156a Rolls converting back to SAM into run_view_test
new 0ef36e8 Adds CRAM conversion using the MD5 REF_CACHE.
new 62102f6 Merge branch 'develop' into develop_testing
new d32c48f Strips out -x / -X tests as -X is deprecated and -x has been repurposed.
new f3ac36f Adds more optional fields in test file, and more -R / -r checks.
new 77cf9d4 Adds tests for the new -x tag stripping option.
new 5c0d1e5 Adds tests for currently undocumented -m and -Q options.
new ed12fe4 Adds some unaligned reads to the samtools view test file.
new 8dc0e7b Minor changes to samtools view test output file names.
new 4c7490b Adds tests for the -s (subsampling) and -@ (threads) options
new 9490d1c Makes filter_sam filter @RG lines when filtering by read group.
new f958e60 Adds comments to explain how the samtools view testing functions work.
new 2db830d Changes *_compare functions to not call passed() or failed().
new f77d2ab Removes dependency on gunzip
new d858395 Merge branch 'develop' into develop_testing
new 21534a1 Adds tests for 'samtools cat'
new b659ed1 Adds more optional tags to alignment lines.
new 79c4892 Add tests for bam2fq.
new eadf538 Adds tests for samtools depad.
new c80a3b0 Adds expected fail and unexpected pass.
new ec3ffad Merge test cases from Rob Davies (PR #162)
new b7ef33b Make xfail/xpass useable by other test subroutines
new e6689c0 Make test_view() -@ tests portable to OS X
new 4afab9a view: Free the header once finished
new 3ad6995 Don't require an index for full-file merges
new b44c5e4 merge,sort: Output BAM, not SAM. Build indexes
new e35361b plot-bamstats: Fixes #183
new f4e96f1 Adds support for outputting stats over the full input size distribution.
new 2bab804 Merge pull request #184 from wtsi-hgi/features/unbounded-is
new d2cad64 Further stats tests
new 502d8dc Remove unusued 'total' functions.
new 6951d73 Merge pull request #186 from wtsi-hgi/issues/warn-unusued-fn
new 517d561 Merge branch 'origin/develop' into develop
new 3518088 The @HD header is optional
new 6557cbc Add "make testclean" target
new c6e3d0b fall over if a bed file given as an option cannot be read
new 402e355 Make stats.c's error() static like the others
new 19d9fe0 Add print_error() and print_error_errno()
new 5ab8804 Merge BED file option error checking (PR #77)
new 8b268c0 Move CDF_MWU_TESTS switch closer to what it controls
new 446c82a Reinstate old-API functions needed by Bio-SamTools Perl module
new cb69971 Support for =X cigars in mpileup, exit on yet untreated cigars.
new f9b1fdc Free all memory in sparse_isize_free
new 3cbc80f stats: Support for =X cigars
new cabd749 Fixes an issue with -i0 involving truncation of insert sizes.
new a59e992 Added expected outputs for stats tests
new d46e675 stats: Prevent nan on output
new 3b739e9 bam_dup1() is now provided by htslib
new 6c3bb9e Convert phase to htslib API
new c2da7c1 Merge phase.c htslibification (PR #190)
new ed70d9c Fixed script for parsing BLAST output
new 267efc4 Fixed a few bugs in blast2sam.pl script, added POD documentation
new 0c87b6e Merge blast2sam.pl improvements (PR #114)
new 2917ccd Clean up merge memleaks
new 802a6bf Silence -Wstrict-prototypes warnings
new 8972694 Create header of common test functions
new 1511278 Add split command to samtools
new 6773e00 Add unit test for bam_split.c's count_rg
new 179e432 Polish bam_split
new 9274bbf Add unit test for bam_split.c's filter_header_rg
new 901dc38 Restructure testing structure to dedupe
new ec49dc4 Add unit test for bam_split.c's parse_args
new 7e311b0 Fix dependencies for test/test.h
new 13bc719 Write files based on the *basename* of the input file
new a587da7 Merge split subcommand (PR #172)
new eb2b309 mpileup: Long options; Custom DP,DV,DP,DP4 format fields on output
new e9ea1ba Removed debugging exit in test.pl; Updated excl/incl long opts
new 702dbd5 mpileup opts: -1,2 now recognised, --ff,rf on popular demand back
new 1083db1 mpileup opts: Added forgotten --ff
new 61cffe1 For your amusement, --ff goes with -2
new d60458f Revert mpileup long options changes
new 3939845 Use hts_set_threads() rather than bgzf_mt()
new 1a46f21 Report sam_write1() and sam_close() errors
new 80f09b4 Added mpileup tests
new 578b207 Mpileup test in Makefile
new a0b45d0 Avoid bashisms
new 49f1859 Abort if an INIT command fails; dispose of _out file
new e948340 Testclean and ignore temporary and output files
new 38eda28 Merge mpileup tests (PR #187)
new 69ab789 Fix long option has_arg inconsistencies
new 3f6b1da mpileup: Absolute INFO/QS to allow incremental calling
new 887e99d Cleanup split memleaks
new e52fe3e Use kstring instead of POSIX 2008's strndup()
new 1da3662 Merge split cleanups (PR #210)
new 16b3d9c Remove our bgzip.c in favour of htslib/bgzip
new 830473c Also clean test/test.o
new 6f4376f Use getopt.h's descriptive constants in long options array
new d9ed1b9 mpileup: support for BAM_CHARD_CLIP cigar
new 93d2ede stats: Simplified usage of --GC-depth, reflen not required
new 1972d96 Reformat usage for 80 columns
new ffa59e7 To free unaccounted_header_name, it must have been malloced
new 47e0bb0 Add code to separate out stdout and stderr in testing
new e4d3791 Make merge take union of commandline and -b inputs and test merge code
new e65f992 Add -b parameter to samtools merge manpage
new ec6c929 Update samtools.1
new eba6ecc Match style for FILE option
new 586b747 Alternate syntax for samtools merge.
new 6fd756f Alternate syntax for samtools merge in stderr message
new eb500de Clarify list is not a literal
new 6f42bf5 Match samtools merge manpage and stderr syntax
new cbbd3a9 Merge branch 'patch-1' of https://github.com/SamStudio8/samtools into merge_unioninput
new 7eb439e Make merge_usage()'s parameter directly understandable
new 1d41868 Merge merge input and doc fixes, test stdout/stderr fixes (PRs #188, #202)
new ba8da93 Fix getline memory leak in test_bam_translate
new fecb1c8 Fix memory leak in test_rtrans_build
new a55624f Fix memory leak in test_trans_tbl_init
new 6cc9736 Add missing fclose of orig_stderr to test_bam_translate
new e89ff5d Fix getline memory leak in test_filter_header_rg
new e068ddc Fix getline missing fcloses in test_parse_args
new e4baec7 Add missing frees to test_parse_args
new 3a71203 Free char* in parsed_opts in test_parse_args
new c433f19 No need to set len=0 before getline
new f430ad3 Free all allocated names from count_RG
new 8fc8247 Close orig_stderr *after* printing final error message
new 39abb1f Merge test harness memory leaks (PR #200)
new 40e4fde Fix calloc() type mismatch
new 971d0e8 Prevent segfault when input file could not be opened
new 8bd7048 Prevent segfault when input file could not be opened
new 4162eb0 Test case fixed by htslib change
new a5ffc51 stats: Check for zero-length cigars (e.g. 0D)
new 813f310 Check for Usage output on stdout (ok) or stderr (expected failure)
new f3b8f76 Migrate ideas from bam2fq from htslib and document
new 7e811ce Miscellaneous code tweaks
new e4b9925 Merge bam2fq improvements and documentation (PR #204)
new f85fab7 Fixes `samtools sort` output to always be BAM
new efe8857 Remove razip source code and remaining vestiges
new 9dff552 Improves performance of `samtools merge` (slightly)
new 1f3ab30 Removes '(forces -S)' from samtools view -T|t usage
new f4e1e04 Updates documentation for `samtools view`
new 3429f6e Tweak `samtools view` documentation formatting
new de89a70 Merge view documentation updates (PR #218)
new e20d0ce Ruthlessly tidied up the examples directory.
new 501e9a7 Revert to ex1.sam.gz; fix mpileup command lines
new 2c921cd Merge examples/ tidy up (PR #226)
new 2f3b4a4 Add seq_cache_populate.pl
new 3b292a4 Add seq_cache_populate.pl (PR #224), add it to "make install"
new 71ab85c Reenable idxstats and convert to htslib
new 08fc571 Update bam_index.o header dependencies
new 4fbe2f0 Merge idxstats htslibification (PR #191)
new 12c985f Call hts_set_fai_filename on the output fd too so that -T has a chance of working. This is one half of the fix necessary for https://github.com/samtools/samtools/issues/144
new 5ae11c7 mpileup: Per-sample rather than cumulative QS. (experimental)
new f85ac7d mpileup: Updated tests
new bc0cae1 Merge branch 'develop' into QS-vs-PL
new 6ec6b81 Merge QS-vs-PL branch into develop
new 2455fd2 Add tests for making CRAM files using samtools view -t/-T
new 6801e6d Add samtools index options to select BAI or CSI
new 0e0ff87 Updated test harness to cope with CRAM now including MD and NM tags in output.
new 0b8f96b mpileup: Reflect change in bcf_hdr_add_sample() usage
new 6c80157 Add output mode parameter to bam_merge_core2 and bam_sort_core_ext
new 2c2fb40 Overhaul samtools sort options and invocation
new 7a2da96 mpileup: Long options
new 1ad9f2e Create a print_usage() function for usage printing
new b47cf4c Reformat usage to (mostly) fit in 80 columns
new a5ba987 Minor rewording of usage to fit in 80 columns
new a93a11d Deprecate `-S`, `-D`, `-V` in favour of `-t DP,DV,SP`
new ce4cfc6 Fix long option has_arg inconsistencies
new 7b8c24e some progress for mpileup documentation
new 1bc231b Use getopt.h's descriptive constants in long options array
new 6e0a670 Remove mpileup -M option, which has never been implemented
new 159e846 Add lowercase synonyms for --VCF etc long options
new ddbd14b Merge mpileup long options (PR #205)
new 1ff7535 mpileup tests: Remove temporary hack, view -C -T now works
new f891933 Merge mpileup test fix: Remove temporary hack, view -C -T now works
new 8e0e91e Fix bug in merge for sorting large files
new 222b94d Fix fixmate's properly paired check, add sam/cram output, add tests
new f593548 Add mpileup --output option to redirect output to a file
new fa9f902 Add mpileup -o FILE as a shorthand for --output
new 773d3bc Updated calling section of samtools man page
new a006f9d mpileup: New optional FORMAT/DPR and INFO/DPR annotations
new b14b219 mpileup: Output symbolic <X> allele instead of VCF-incompatible X
new 39f16d8 Save the right error text (fixes cut-and-pasto)
new 5ec815e Added CRAM reference information and an example.
new 0b94612 Report file opening failures rather than crashing
new 978c2a8 Note explicitly that merge output remains sorted
new 0248f39 Report errno for file opening failures
new 11b4087 Implement bam2depth directly against the htslib API
new 7ace6c2 Report index and region failures rather than crashing
new 0f969b8 mpileup: Support for cigar operator "P", resolves #243
new 17b06ad mpileup: Do not crash on non-existent files, resolves #244
new 8030ea3 mpileup: Fix in DPR calculation - there can be
new 5366fce Clear bcf_callret1_t to avoid segfault
new f4320cd tview: Recover from incomplete fai files
new 4735dbb Update documentation for samtools merge
new 27d8e0c Fix idxstats error and add test
new 57372fc mpileup: Support for cigar operation N
new 5c3a553 add tests for samtools index with large chromosome
new 9c4d66a Omit control files and README.md from release tarballs
new 6684f78 Update license file
new d366755 Add licensing boilerplate
new 21680da Update copyright years to reflect historic changes
new 62c3458 Add copyright notices and licensing boilerplate
new 7006245 Add copyright notices and licensing boilerplate
new 85cab3d Add copyright notices and licensing boilerplate
new 02a6359 Update copyright years and reformat licensing boilerplate
new 3ff81ed Update copyright years and reformat licensing boilerplate
new a869c9a Fix copyright notices and reformat licensing boilerplate
new 8da9ef2 Add copyright notices and licensing boilerplate
new 0be3a71 Add copyright notices and licensing boilerplate
new 293e8ce Reformat copyright notices and licensing boilerplate
new 4363c1f Add copyright notices and licensing boilerplate
new 1d7aecf Merge copyright notice and licensing boilerplate additions
new fcb8af0 Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
new bbe85a9 Ensure installation directories are world-executable
new e3f59f8 Man page minor edit and whitespace canonicalisation
new 88f7ca9 plot-bamstats: better support for plots of single-read bams
new 67a964d stats: Accept string flags with -f/F
new 3ddba70 plot-bamstats: Generate summary html page
new 9662d2d plot-bamstats: Use 0x1 rather than 0x2 flag to detect paired-end
new 5943ad7 plot-bamstats: fixes in create_html and gz input
new 433f887 Merge bug fixes for #183 and #262
new c20d4bb Use "%s+htslib-%s" version format
new ad732cd Add basic INSTALL and README files
new 5370fe9 Release 1.0: first htslib-based samtools release
new 3dabde5 Merge branch 'master' into debian/unstable
new 89a7c0e Merge branch 'debian/unstable' of git+ssh://git.debian.org/git/debian-med/samtools into debian/unstable
The 366 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 | 5 +
.gitignore | 4 +-
AUTHORS | 10 +-
INSTALL | 36 +-
LICENSE | 33 +
Makefile | 170 +-
NEWS | 14 +
README | 5 +
README.md | 6 +-
bam.c | 263 +-
bam.h | 750 +-
bam2bcf.c | 528 +-
bam2bcf.h | 110 +-
bam2bcf_indel.c | 891 +-
bam2depth.c | 218 +-
bam_aux.c | 83 +-
bam_cat.c | 47 +-
bam_color.c | 226 +-
bam_endian.h | 52 +-
bam_flags.c | 35 +-
bam_import.c | 76 +-
bam_index.c | 143 +-
bam_lpileup.c | 315 +-
bam_lpileup.h | 57 +
bam_mate.c | 462 +-
bam_md.c | 705 +-
bam_plbuf.c | 67 +
bam_plbuf.h | 55 +
bam_plcmd.c | 1121 +-
bam_reheader.c | 109 +-
bam_rmdup.c | 327 +-
bam_rmdupse.c | 255 +-
bam_sort.c | 1550 +-
bam_split.c | 509 +
bam_stat.c | 150 +-
bam_tview.c | 760 +-
bam_tview.h | 70 +-
bam_tview_curses.c | 423 +-
bam_tview_html.c | 496 +-
bamshuf.c | 223 +-
bamtk.c | 172 +-
bedcov.c | 226 +-
bedidx.c | 322 +-
bgzip.c | 265 -
cut_target.c | 321 +-
errmod.c | 253 +-
errmod.h | 37 +-
examples/.gitignore | 1 +
examples/00README.txt | 40 +-
examples/Makefile | 50 -
examples/bam2bed.c | 51 -
examples/calDepth.c | 62 -
examples/chk_indel.c | 83 -
faidx.c | 39 +-
kaln.c | 2 +-
kaln.h | 2 +-
kprobaln.c | 2 +-
kprobaln.h | 2 +-
misc/HmmGlocal.java | 366 +-
misc/ace2sam.c | 384 +-
misc/blast2sam.pl | 204 +-
misc/bowtie2sam.pl | 97 +-
misc/export2sam.pl | 22 +-
misc/interpolate_sam.pl | 41 +-
misc/maq2sam.c | 262 +-
misc/md5.c | 2 +
misc/md5fa.c | 108 +-
misc/novo2sam.pl | 326 +-
misc/plot-bamstats | 487 +-
misc/psl2sam.pl | 60 +-
misc/r2plot.lua | 90 +-
misc/sam2vcf.pl | 85 +-
misc/samtools.pl | 506 +-
misc/seq_cache_populate.pl | 317 +
misc/soap2sam.pl | 91 +-
misc/varfilter.py | 304 +-
misc/vcfutils.lua | 1124 +-
misc/wgsim.c | 598 +-
misc/wgsim_eval.pl | 150 +-
misc/zoom2sam.pl | 73 +-
padding.c | 846 +-
phase.c | 1186 +-
razip.c | 142 -
sam.c | 137 +-
sam.h | 142 +-
sam_header.c | 154 +-
sam_header.h | 52 +-
sam_view.c | 1042 +-
sample.c | 171 +-
sample.h | 30 +-
samtools.1 | 908 +-
samtools.h | 39 +-
stats.c | 508 +-
stats_isize.c | 219 +
stats_isize.h | 83 +
test/dat/bam2fq.001.sam | 64 +
test/dat/cat.hdr | 25 +
test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468 | 1 +
test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437 | 1 +
test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4 | 1 +
test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b | 1 +
test/dat/depad.001.fa | 2 +
test/dat/depad.001.fa.fai | 1 +
test/dat/depad.001p.sam | 138 +
test/dat/depad.001u.sam | 138 +
test/dat/empty.expected | 0
test/dat/large_chrom.out | 6 +
test/dat/large_chrom.sam | 63 +
test/dat/large_chrom_bai_index.err | 1 +
test/dat/mpileup.1.sam | 1016 +
test/dat/mpileup.2.sam | 248 +
test/dat/mpileup.3.sam | 250 +
test/dat/mpileup.err.1 | 2 +
test/dat/mpileup.out.1 | 68 +-
test/dat/mpileup.out.2 | 1094 +-
test/dat/test_input_1_a.bam | Bin 0 -> 758 bytes
test/dat/test_input_1_a.bam.bai | Bin 0 -> 264 bytes
test/dat/test_input_1_a.sam | 28 +
test/dat/test_input_1_b.bam | Bin 0 -> 687 bytes
test/dat/test_input_1_b.bam.bai | Bin 0 -> 192 bytes
test/dat/test_input_1_b.sam | 24 +
test/dat/test_input_1_c.bam | Bin 0 -> 655 bytes
test/dat/test_input_1_c.bam.bai | Bin 0 -> 176 bytes
test/dat/test_input_1_c.sam | 22 +
test/dat/view.001.01.bed | 27 +
test/dat/view.001.02.bed | 22 +
test/dat/view.001.fa | 4 +
test/dat/view.001.fa.fai | 2 +
test/dat/view.001.sam | 62 +
test/dat/view.002.01.bed | 25 +
test/dat/view.002.02.bed | 30 +
test/dat/view.002.fa | 2 +
test/dat/view.002.fa.fai | 1 +
test/dat/view.002.sam | 83 +
test/dat/view.003.expected.sam | 39 +
test/dat/view.003.sam | 39 +
test/fixmate/1_coord_sort.sam.expected | 0
test/fixmate/1_coord_sort.sam.expected.err | 2 +
..._overflow.sam => 2_isize_overflow.sam.expected} | 12 +-
test/fixmate/3_reverse_read_pp_lt.sam | 5 +
test/fixmate/3_reverse_read_pp_lt.sam.expected | 5 +
test/fixmate/4_reverse_read_pp_equal.sam | 5 +
test/fixmate/4_reverse_read_pp_equal.sam.expected | 5 +
test/idxstats/test_input_1_a.bam.expected | 5 +
test/idxstats/test_input_1_a.bam.expected.err | 0
test/merge/.gitignore | 6 +
test/merge/2.merge.expected.bam | Bin 0 -> 1181 bytes
test/merge/3.merge.expected.bam | Bin 0 -> 1199 bytes
test/merge/3.merge.expected.err | 5 +
test/merge/test_3.fofn | 2 +
test/merge/test_bam_translate.c | 591 +
test/merge/test_header.sam | 11 +
test/merge/test_pretty_header.c | 87 +
test/merge/test_rtrans_build.c | 118 +
test/merge/test_trans_tbl_init.c | 471 +
test/mpileup/.gitignore | 11 +
test/mpileup/1read.bam | Bin 0 -> 525 bytes
test/mpileup/1read.sam | 1 +
test/mpileup/anomalous.sam | 6 +
test/mpileup/bcf_filter.sh | 29 +
test/mpileup/c1#ID.bam | Bin 0 -> 293 bytes
test/mpileup/c1#ID2.bam | Bin 0 -> 377 bytes
test/mpileup/c1#clip.bam | Bin 0 -> 265 bytes
test/mpileup/c1#pad1.bam | Bin 0 -> 299 bytes
test/mpileup/c1#pad2.bam | Bin 0 -> 349 bytes
test/mpileup/c1#pad3.bam | Bin 0 -> 382 bytes
test/mpileup/c1.fa | 4 +
test/mpileup/c1.fa.fai | 2 +
test/mpileup/ce#5b.bam | Bin 0 -> 557 bytes
test/mpileup/ce#5b.bam.bai | Bin 0 -> 416 bytes
test/mpileup/ce#5b.cram | Bin 0 -> 13183 bytes
test/mpileup/ce#5b.cram.crai | Bin 0 -> 75 bytes
test/mpileup/ce#5b.sam | 12 +
test/mpileup/ce#large_seq.bam | Bin 0 -> 345315 bytes
test/mpileup/ce#unmap.bam | Bin 0 -> 233 bytes
test/mpileup/ce#unmap1.bam | Bin 0 -> 896 bytes
test/mpileup/ce#unmap2.bam | Bin 0 -> 1344 bytes
test/mpileup/ce.fa | 20803 +++++++++++++++++++
test/mpileup/ce.fa.fai | 7 +
test/mpileup/deep.sam | 9001 ++++++++
test/mpileup/expected/1.out.xz | Bin 0 -> 1336220 bytes
test/mpileup/expected/10.out | 40 +
test/mpileup/expected/11.out | 9 +
test/mpileup/expected/12.out | 9 +
test/mpileup/expected/13.out | 4101 ++++
test/mpileup/expected/14.out | 4101 ++++
test/mpileup/expected/15.out | 4101 ++++
test/mpileup/expected/16.out | 4101 ++++
test/mpileup/expected/17.out | 4101 ++++
test/mpileup/expected/18.out | 4101 ++++
test/mpileup/expected/19.out | 4101 ++++
test/mpileup/expected/2.out | 0
test/mpileup/expected/20.out | 4101 ++++
test/mpileup/expected/21.out | 4101 ++++
test/mpileup/expected/22.out | 4101 ++++
test/mpileup/expected/23.out | 150 +
test/mpileup/expected/24.out | 150 +
test/mpileup/expected/25.out | 150 +
test/mpileup/expected/26.out | 100 +
test/mpileup/expected/27.out | 100 +
test/mpileup/expected/28.out | 4101 ++++
test/mpileup/expected/29.out | 0
test/mpileup/expected/3.out | 0
test/mpileup/expected/30.out | 100 +
test/mpileup/expected/31.out | 100 +
test/mpileup/expected/32.out | 100 +
test/mpileup/expected/33.out | 12 +
test/mpileup/expected/34.out | 12 +
test/mpileup/expected/35.out | 3397 +++
test/mpileup/expected/37.out | 4101 ++++
test/mpileup/expected/38.out | 102 +
test/mpileup/expected/39.out | 11 +
test/mpileup/expected/4.out | 101 +
test/mpileup/expected/40.out | 84 +
test/mpileup/expected/41.out | 21 +
test/mpileup/expected/42.out | 0
test/mpileup/expected/43.out | 3893 ++++
test/mpileup/expected/44.out | 3893 ++++
test/mpileup/expected/45.out | 4097 ++++
test/mpileup/expected/46.out | 4097 ++++
test/mpileup/expected/47.out | 1 +
test/mpileup/expected/48.out | 4104 ++++
test/mpileup/expected/49.out | 4104 ++++
test/mpileup/expected/5.out | 10 +
test/mpileup/expected/50.out | 4104 ++++
test/mpileup/expected/51.out | 4104 ++++
test/mpileup/expected/52.out | 1 +
test/mpileup/expected/53.out | 1 +
test/mpileup/expected/54.out | 1 +
test/mpileup/expected/55.out | 1 +
test/mpileup/expected/56.out | 1 +
test/mpileup/expected/57.out | 1 +
test/mpileup/expected/58.out | 1 +
test/mpileup/expected/59.out | 1 +
test/mpileup/expected/6.out | 10 +
test/mpileup/expected/60.out | 0
test/mpileup/expected/61.out | 1 +
test/mpileup/expected/62.out | 0
test/mpileup/expected/63.out | 1 +
test/mpileup/expected/64.out | 0
test/mpileup/expected/65.out | 1 +
test/mpileup/expected/66.out | 0
test/mpileup/expected/67.out | 1 +
test/mpileup/expected/68.out | 0
test/mpileup/expected/69.out | 0
test/mpileup/expected/7.out | 10 +
test/mpileup/expected/70.out | 1 +
test/mpileup/expected/71.out | 1 +
test/mpileup/expected/72.out | 0
test/mpileup/expected/73.out | 1 +
test/mpileup/expected/74.out | 0
test/mpileup/expected/75.out | 1 +
test/mpileup/expected/76.out | 4101 ++++
test/mpileup/expected/77.out | 4101 ++++
test/mpileup/expected/8.out | 5 +
test/mpileup/expected/9.out | 10 +
test/mpileup/indels.sam | 9 +
test/mpileup/mpileup-E.bam | Bin 0 -> 280 bytes
test/{dat => mpileup}/mpileup.1.bam | Bin
test/mpileup/mpileup.1.bam.bai | Bin 0 -> 776 bytes
test/{dat => mpileup}/mpileup.2.bam | Bin
test/{dat => mpileup}/mpileup.3.bam | Bin
test/{dat => mpileup}/mpileup.ref.fa | 0
test/{dat => mpileup}/mpileup.ref.fa.fai | 0
test/mpileup/mpileup.reg | 144 +
test/mpileup/overlap50.sam | 5 +
test/mpileup/overlapIllumina.bam | Bin 0 -> 583 bytes
test/mpileup/regions | 10 +
test/mpileup/regression.sh | 149 +
test/mpileup/xx#minimal.bam | Bin 0 -> 215 bytes
test/mpileup/xx#triplet.bam | Bin 0 -> 247 bytes
test/mpileup/xx.fa | 5 +
test/mpileup/xx.fa.fai | 2 +
test/split/.gitignore | 4 +
test/split/test_count_rg.c | 124 +
test/split/test_expand_format_string.c | 124 +
test/split/test_filter_header_rg.c | 191 +
test/split/test_parse_args.c | 215 +
test/stat/1.stats.expected | 299 +
test/stat/1_map_cigar.sam | 5 +
test/stat/2.stats.expected | 299 +
test/stat/2_equal_cigar_full_seq.sam | 5 +
test/stat/3.stats.expected | 262 +
test/stat/3_map_cigar_equal_seq.sam | 5 +
test/stat/4.stats.expected | 299 +
test/stat/4_X_cigar_full_seq.sam | 5 +
test/stat/5.stats.expected | 301 +
test/stat/5_insert_cigar.sam | 5 +
test/stat/6.stats.expected | 301 +
test/stat/test.fa | 3 +
test/stat/test.fa.fai | 1 +
test/test.c | 53 +
COPYING => test/test.h | 28 +-
test/test.pl | 1978 +-
test/tview/test_get_rg_sample.c | 81 +
295 files changed, 147929 insertions(+), 10984 deletions(-)
create mode 100644 LICENSE
create mode 100644 README
create mode 100644 bam_lpileup.h
create mode 100644 bam_plbuf.c
create mode 100644 bam_plbuf.h
create mode 100644 bam_split.c
delete mode 100644 bgzip.c
delete mode 100644 examples/Makefile
delete mode 100644 examples/bam2bed.c
delete mode 100644 examples/calDepth.c
delete mode 100644 examples/chk_indel.c
create mode 100755 misc/seq_cache_populate.pl
delete mode 100644 razip.c
create mode 100644 stats_isize.c
create mode 100644 stats_isize.h
create mode 100644 test/dat/bam2fq.001.sam
create mode 100644 test/dat/cat.hdr
create mode 100644 test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468
create mode 100644 test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437
create mode 100644 test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4
create mode 100644 test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b
create mode 100644 test/dat/depad.001.fa
create mode 100644 test/dat/depad.001.fa.fai
create mode 100644 test/dat/depad.001p.sam
create mode 100644 test/dat/depad.001u.sam
create mode 100644 test/dat/empty.expected
create mode 100644 test/dat/large_chrom.out
create mode 100644 test/dat/large_chrom.sam
create mode 100644 test/dat/large_chrom_bai_index.err
create mode 100644 test/dat/mpileup.1.sam
create mode 100644 test/dat/mpileup.2.sam
create mode 100644 test/dat/mpileup.3.sam
create mode 100644 test/dat/mpileup.err.1
create mode 100644 test/dat/test_input_1_a.bam
create mode 100644 test/dat/test_input_1_a.bam.bai
create mode 100644 test/dat/test_input_1_a.sam
create mode 100644 test/dat/test_input_1_b.bam
create mode 100644 test/dat/test_input_1_b.bam.bai
create mode 100644 test/dat/test_input_1_b.sam
create mode 100644 test/dat/test_input_1_c.bam
create mode 100644 test/dat/test_input_1_c.bam.bai
create mode 100644 test/dat/test_input_1_c.sam
create mode 100644 test/dat/view.001.01.bed
create mode 100644 test/dat/view.001.02.bed
create mode 100644 test/dat/view.001.fa
create mode 100644 test/dat/view.001.fa.fai
create mode 100644 test/dat/view.001.sam
create mode 100644 test/dat/view.002.01.bed
create mode 100644 test/dat/view.002.02.bed
create mode 100644 test/dat/view.002.fa
create mode 100644 test/dat/view.002.fa.fai
create mode 100644 test/dat/view.002.sam
create mode 100644 test/dat/view.003.expected.sam
create mode 100644 test/dat/view.003.sam
create mode 100644 test/fixmate/1_coord_sort.sam.expected
create mode 100644 test/fixmate/1_coord_sort.sam.expected.err
copy test/fixmate/{2_isize_overflow.sam => 2_isize_overflow.sam.expected} (64%)
create mode 100644 test/fixmate/3_reverse_read_pp_lt.sam
create mode 100644 test/fixmate/3_reverse_read_pp_lt.sam.expected
create mode 100644 test/fixmate/4_reverse_read_pp_equal.sam
create mode 100644 test/fixmate/4_reverse_read_pp_equal.sam.expected
create mode 100644 test/idxstats/test_input_1_a.bam.expected
create mode 100644 test/idxstats/test_input_1_a.bam.expected.err
create mode 100644 test/merge/.gitignore
create mode 100644 test/merge/2.merge.expected.bam
create mode 100644 test/merge/3.merge.expected.bam
create mode 100644 test/merge/3.merge.expected.err
create mode 100644 test/merge/test_3.fofn
create mode 100644 test/merge/test_bam_translate.c
create mode 100644 test/merge/test_header.sam
create mode 100644 test/merge/test_pretty_header.c
create mode 100644 test/merge/test_rtrans_build.c
create mode 100644 test/merge/test_trans_tbl_init.c
create mode 100644 test/mpileup/.gitignore
create mode 100644 test/mpileup/1read.bam
create mode 100644 test/mpileup/1read.sam
create mode 100644 test/mpileup/anomalous.sam
create mode 100755 test/mpileup/bcf_filter.sh
create mode 100644 test/mpileup/c1#ID.bam
create mode 100644 test/mpileup/c1#ID2.bam
create mode 100644 test/mpileup/c1#clip.bam
create mode 100644 test/mpileup/c1#pad1.bam
create mode 100644 test/mpileup/c1#pad2.bam
create mode 100644 test/mpileup/c1#pad3.bam
create mode 100644 test/mpileup/c1.fa
create mode 100644 test/mpileup/c1.fa.fai
create mode 100644 test/mpileup/ce#5b.bam
create mode 100644 test/mpileup/ce#5b.bam.bai
create mode 100644 test/mpileup/ce#5b.cram
create mode 100644 test/mpileup/ce#5b.cram.crai
create mode 100644 test/mpileup/ce#5b.sam
create mode 100644 test/mpileup/ce#large_seq.bam
create mode 100644 test/mpileup/ce#unmap.bam
create mode 100644 test/mpileup/ce#unmap1.bam
create mode 100644 test/mpileup/ce#unmap2.bam
create mode 100644 test/mpileup/ce.fa
create mode 100644 test/mpileup/ce.fa.fai
create mode 100644 test/mpileup/deep.sam
create mode 100644 test/mpileup/expected/1.out.xz
create mode 100644 test/mpileup/expected/10.out
create mode 100644 test/mpileup/expected/11.out
create mode 100644 test/mpileup/expected/12.out
create mode 100644 test/mpileup/expected/13.out
create mode 100644 test/mpileup/expected/14.out
create mode 100644 test/mpileup/expected/15.out
create mode 100644 test/mpileup/expected/16.out
create mode 100644 test/mpileup/expected/17.out
create mode 100644 test/mpileup/expected/18.out
create mode 100644 test/mpileup/expected/19.out
create mode 100644 test/mpileup/expected/2.out
create mode 100644 test/mpileup/expected/20.out
create mode 100644 test/mpileup/expected/21.out
create mode 100644 test/mpileup/expected/22.out
create mode 100644 test/mpileup/expected/23.out
create mode 100644 test/mpileup/expected/24.out
create mode 100644 test/mpileup/expected/25.out
create mode 100644 test/mpileup/expected/26.out
create mode 100644 test/mpileup/expected/27.out
create mode 100644 test/mpileup/expected/28.out
create mode 100644 test/mpileup/expected/29.out
create mode 100644 test/mpileup/expected/3.out
create mode 100644 test/mpileup/expected/30.out
create mode 100644 test/mpileup/expected/31.out
create mode 100644 test/mpileup/expected/32.out
create mode 100644 test/mpileup/expected/33.out
create mode 100644 test/mpileup/expected/34.out
create mode 100644 test/mpileup/expected/35.out
create mode 100644 test/mpileup/expected/37.out
create mode 100644 test/mpileup/expected/38.out
create mode 100644 test/mpileup/expected/39.out
create mode 100644 test/mpileup/expected/4.out
create mode 100644 test/mpileup/expected/40.out
create mode 100644 test/mpileup/expected/41.out
create mode 100644 test/mpileup/expected/42.out
create mode 100644 test/mpileup/expected/43.out
create mode 100644 test/mpileup/expected/44.out
create mode 100644 test/mpileup/expected/45.out
create mode 100644 test/mpileup/expected/46.out
create mode 100644 test/mpileup/expected/47.out
create mode 100644 test/mpileup/expected/48.out
create mode 100644 test/mpileup/expected/49.out
create mode 100644 test/mpileup/expected/5.out
create mode 100644 test/mpileup/expected/50.out
create mode 100644 test/mpileup/expected/51.out
create mode 100644 test/mpileup/expected/52.out
create mode 100644 test/mpileup/expected/53.out
create mode 100644 test/mpileup/expected/54.out
create mode 100644 test/mpileup/expected/55.out
create mode 100644 test/mpileup/expected/56.out
create mode 100644 test/mpileup/expected/57.out
create mode 100644 test/mpileup/expected/58.out
create mode 100644 test/mpileup/expected/59.out
create mode 100644 test/mpileup/expected/6.out
create mode 100644 test/mpileup/expected/60.out
create mode 100644 test/mpileup/expected/61.out
create mode 100644 test/mpileup/expected/62.out
create mode 100644 test/mpileup/expected/63.out
create mode 100644 test/mpileup/expected/64.out
create mode 100644 test/mpileup/expected/65.out
create mode 100644 test/mpileup/expected/66.out
create mode 100644 test/mpileup/expected/67.out
create mode 100644 test/mpileup/expected/68.out
create mode 100644 test/mpileup/expected/69.out
create mode 100644 test/mpileup/expected/7.out
create mode 100644 test/mpileup/expected/70.out
create mode 100644 test/mpileup/expected/71.out
create mode 100644 test/mpileup/expected/72.out
create mode 100644 test/mpileup/expected/73.out
create mode 100644 test/mpileup/expected/74.out
create mode 100644 test/mpileup/expected/75.out
create mode 100644 test/mpileup/expected/76.out
create mode 100644 test/mpileup/expected/77.out
create mode 100644 test/mpileup/expected/8.out
create mode 100644 test/mpileup/expected/9.out
create mode 100644 test/mpileup/indels.sam
create mode 100644 test/mpileup/mpileup-E.bam
rename test/{dat => mpileup}/mpileup.1.bam (100%)
create mode 100644 test/mpileup/mpileup.1.bam.bai
rename test/{dat => mpileup}/mpileup.2.bam (100%)
rename test/{dat => mpileup}/mpileup.3.bam (100%)
copy test/{dat => mpileup}/mpileup.ref.fa (100%)
copy test/{dat => mpileup}/mpileup.ref.fa.fai (100%)
create mode 100644 test/mpileup/mpileup.reg
create mode 100644 test/mpileup/overlap50.sam
create mode 100644 test/mpileup/overlapIllumina.bam
create mode 100644 test/mpileup/regions
create mode 100755 test/mpileup/regression.sh
create mode 100644 test/mpileup/xx#minimal.bam
create mode 100644 test/mpileup/xx#triplet.bam
create mode 100644 test/mpileup/xx.fa
create mode 100644 test/mpileup/xx.fa.fai
create mode 100644 test/split/.gitignore
create mode 100644 test/split/test_count_rg.c
create mode 100644 test/split/test_expand_format_string.c
create mode 100644 test/split/test_filter_header_rg.c
create mode 100644 test/split/test_parse_args.c
create mode 100644 test/stat/1.stats.expected
create mode 100644 test/stat/1_map_cigar.sam
create mode 100644 test/stat/2.stats.expected
create mode 100644 test/stat/2_equal_cigar_full_seq.sam
create mode 100644 test/stat/3.stats.expected
create mode 100644 test/stat/3_map_cigar_equal_seq.sam
create mode 100644 test/stat/4.stats.expected
create mode 100644 test/stat/4_X_cigar_full_seq.sam
create mode 100644 test/stat/5.stats.expected
create mode 100644 test/stat/5_insert_cigar.sam
create mode 100644 test/stat/6.stats.expected
create mode 100644 test/stat/test.fa
create mode 100644 test/stat/test.fa.fai
create mode 100644 test/test.c
rename COPYING => test/test.h (61%)
create mode 100644 test/tview/test_get_rg_sample.c
--
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