[med-svn] samtools annotated tag 1.0 created (now 489c27f)
Charles Plessy
plessy at moszumanska.debian.org
Mon Aug 18 01:39:59 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to annotated tag 1.0
in repository samtools.
at 489c27f (tag)
tagging 5370fe9d469c8b123bec1638dd1e3d2f92308bd6 (commit)
replaces 0.1.20
tagged by John Marshall
on Fri Aug 15 11:34:39 2014 +0100
- Log -----------------------------------------------------------------
First HTSlib-based Samtools release
Christian Brueffer (1):
Fix typos in the manpage.
Erik Aronesty (1):
add -U FILE to output unselected reads for pipelin
James Bonfield (6):
Added mpileup tests
Mpileup test in Makefile
Ruthlessly tidied up the examples directory.
Call hts_set_fai_filename on the output fd too so that -T has a chance
Updated test harness to cope with CRAM now including MD and NM tags in
Added CRAM reference information and an example.
John Marshall (179):
Merge trivial changes from htslib's knetfile.c
Use htslib's klib instead of our own
Use htslib's bgzf.h, faidx.h, and razf.h
Ensure examples/calDepth compiles
Use all-bgzf_*() functions instead of a mixture
bamshuf.c already uses the htslib API
Use the generic bam_write1() here
Remove bam_nt16_nt4_table from the public header
Call bam_remove_B() explicitly
Temporarily comment out header manipulation
Replace libbam with htslib API wrappers
Move bam_fetch() to libbam's bam.c
Merge branch 'develop' into with-htslib
Include htslib in our build directory
Include htslib rules and add header dependencies
Fix buglet: initialise the kstring_t
Updates for recent htslib changes (9dfcc31)
Merge branch 'with-htslib' into develop
Remove recursive make for "misc" subdirectory
Tidy up makefile
Fix typo, remove razip vestige [minor]
Also run our tests
Set Git attributes for BAM files in the repository
Add help command and --version options
Write samtools --help output to stdout
Ensure $HTSDIR is used by "make test" too
Remove bcftools, SAM, and VCF sections from man page
Detect input format and add samtools view -C option
Add "make install" target
Add omitted non-Perl misc/ programs
Correct reverse complements of CG and AT
Fix old API samopen() wrapper fn_aux bugs
Add an unoptimised GCC C99 build
Use static inline, not just inline
Update for htslib API change: hts_open() has only two parameters
Merge branch fixmate of git://github.com/mp15/samtools
Fix typo; fixes #85.
Merge pull request #91 from mp15/fixmate
Reinstate bam_iter_read(iter=NULL) reading the whole file
Fix CRLF-style line termination
Free the outer struct last
Merge branch master of git://github.com/leecbaker/samtools
Use floor(x+0.5) instead of C99's round()
Rearrange (so tags can see main_depth()) [minor]
Remove incorrect parameter check
Fail when tests fail
Usage message tweaks to satisfy test/test.pl's test_usage()
Implement view & bam2fq directly against the htslib API
Use new sam_itr_*() htslib API for BAM/CRAM iterators
[bedcov] Use the htslib API directly, now works with BAM or CRAM files
Use htslib's bam_endpos() instead of copied old bam_calend() code
Merge pull request #118, fixing man page typos
Merge pull request #141 from sb10/develop
Merge pull request #109 from aux_tag_strip of github.com/mp15/samtools
Merge pull request #106, properly-paired flag statistics
Shut up, clang!
Use htslib facilities instead of bam_parse_region()
Revert unnecessary changes on tview branch
Use sam_itr_*()/etc and enable compiling with current htslib
Fix tview-related dependencies
Merge pull request #93, convert tview to htslib API
Use sam_itr_*()/etc, enabling tview on CRAM files
Fix "Usage: ..." message
Merge #148, links to 'sister' projects (but omitting ourself)
Update dependencies and define _GNU_SOURCE only for bam_sort.o
Use htslib facilities instead of bam_parse_region() etc
Make I/O redirection portable (to Linux)
Add test/merge/* test programs to main Makefile
Merge pull request #70, merge improvements
Create xfreopen() utility instead of duplicating code
Use kstring instead of asprintf()
Merge asprintf()->kstring rewrite and warning fixes (#161)
Fix buffer overflow
Use kstring instead of strndup()
Extant code in sam_view.c does not use Yoda conditions
Merge read group filtering changes (PR #164)
Print dummy column for MAPQ for mpileup -s
Disconnect clean-htslib from clean target
Don't malloc the kstring_t; minor changes to the big comment
Merge BED file parsing improvements (PR #165)
Merge view -U option (PR #177), also adding it to the man page
Merge view subsampling randomness (PR #167, fixes #160)
Merge test cases from Rob Davies (PR #162)
Make xfail/xpass useable by other test subroutines
Make test_view() -@ tests portable to OS X
Don't require an index for full-file merges
Merge branch 'origin/develop' into develop
The @HD header is optional
Add "make testclean" target
Make stats.c's error() static like the others
Add print_error() and print_error_errno()
Merge BED file option error checking (PR #77)
Move CDF_MWU_TESTS switch closer to what it controls
Fix dependencies for test/test.h
Write files based on the *basename* of the input file
Reinstate old-API functions needed by Bio-SamTools Perl module
bam_dup1() is now provided by htslib
Merge phase.c htslibification (PR #190)
Merge blast2sam.pl improvements (PR #114)
Silence -Wstrict-prototypes warnings
Merge split subcommand (PR #172)
Revert mpileup long options changes
Avoid bashisms
Create a print_usage() function for usage printing
Abort if an INIT command fails; dispose of _out file
Reformat usage to (mostly) fit in 80 columns
Testclean and ignore temporary and output files
Minor rewording of usage to fit in 80 columns
Use hts_set_threads() rather than bgzf_mt()
Report sam_write1() and sam_close() errors
Merge mpileup tests (PR #187)
Fix long option has_arg inconsistencies
Fix long option has_arg inconsistencies
Use kstring instead of POSIX 2008's strndup()
Merge split cleanups (PR #210)
Remove our bgzip.c in favour of htslib/bgzip
Also clean test/test.o
Use getopt.h's descriptive constants in long options array
Use getopt.h's descriptive constants in long options array
Reformat usage for 80 columns
To free unaccounted_header_name, it must have been malloced
Make merge_usage()'s parameter directly understandable
Merge merge input and doc fixes, test stdout/stderr fixes (PRs #188, #202)
Close orig_stderr *after* printing final error message
Merge test harness memory leaks (PR #200)
Fix calloc() type mismatch
Prevent segfault when input file could not be opened
Prevent segfault when input file could not be opened
Test case fixed by htslib change
Miscellaneous code tweaks
Check for Usage output on stdout (ok) or stderr (expected failure)
Merge bam2fq improvements and documentation (PR #204)
Remove mpileup -M option, which has never been implemented
Remove razip source code and remaining vestiges
Tweak `samtools view` documentation formatting
Merge view documentation updates (PR #218)
Revert to ex1.sam.gz; fix mpileup command lines
Merge examples/ tidy up (PR #226)
Add lowercase synonyms for --VCF etc long options
Add seq_cache_populate.pl (PR #224), add it to "make install"
Update bam_index.o header dependencies
Merge idxstats htslibification (PR #191)
Merge QS-vs-PL branch into develop
Add samtools index options to select BAI or CSI
Add output mode parameter to bam_merge_core2 and bam_sort_core_ext
Overhaul samtools sort options and invocation
Merge mpileup long options (PR #205)
Merge mpileup test fix: Remove temporary hack, view -C -T now works
Add mpileup --output option to redirect output to a file
Add mpileup -o FILE as a shorthand for --output
Save the right error text (fixes cut-and-pasto)
Update license file
Report file opening failures rather than crashing
Note explicitly that merge output remains sorted
Report errno for file opening failures
Implement bam2depth directly against the htslib API
Report index and region failures rather than crashing
Clear bcf_callret1_t to avoid segfault
Omit control files and README.md from release tarballs
Add licensing boilerplate
Update copyright years to reflect historic changes
Add copyright notices and licensing boilerplate
Add copyright notices and licensing boilerplate
Add copyright notices and licensing boilerplate
Update copyright years and reformat licensing boilerplate
Update copyright years and reformat licensing boilerplate
Fix copyright notices and reformat licensing boilerplate
Add copyright notices and licensing boilerplate
Add copyright notices and licensing boilerplate
Reformat copyright notices and licensing boilerplate
Add copyright notices and licensing boilerplate
Merge copyright notice and licensing boilerplate additions
Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
Ensure installation directories are world-executable
Man page minor edit and whitespace canonicalisation
Merge bug fixes for #183 and #262
Use "%s+htslib-%s" version format
Add basic INSTALL and README files
Release 1.0: first htslib-based samtools release
Joshua Randall (7):
Fixed GCC section so that read cycle column begins with 1 instead of 0.
Adds tests for usage message for samtools and all subcommands
Modifies test.pl so that it exits with non-zero status if any tests fail.
Fixes `samtools sort` output to always be BAM
Removes '(forces -S)' from samtools view -T|t usage
Updates documentation for `samtools view`
Improves performance of `samtools merge` (slightly)
Lee Baker (2):
Fix compilation with the Clang compiler.
Fix type mismatches between types in sizeof() in malloc/calloc/realloc calls. This generates a warning in the clang analyzer, designed to catch incorrectly sized memory allocations.
Martin O. Pollard (24):
Convert samtools stats to htslib
Add Test files for stats
Fix compiler warning in stats
Enable tests for samtools stats
Create header of common test functions
Add split command to samtools
Add unit test for bam_split.c's count_rg
Polish bam_split
Add unit test for bam_split.c's filter_header_rg
Restructure testing structure to dedupe
Add unit test for bam_split.c's parse_args
Further stats tests
Convert phase to htslib API
Reenable idxstats and convert to htslib
Clean up merge memleaks
Add code to separate out stdout and stderr in testing
Make merge take union of commandline and -b inputs and test merge code
Merge branch 'patch-1' of https://github.com/SamStudio8/samtools into merge_unioninput
Migrate ideas from bam2fq from htslib and document
Cleanup split memleaks
Fix bug in merge for sorting large files
Fix fixmate's properly paired check, add sam/cram output, add tests
Update documentation for samtools merge
Fix idxstats error and add test
Martin Pollard (91):
Fix whitespace inconsistancy and add license to bam_tview.c.
Some initial comments whilst I think how to fix this.
Split out syncing of mate flags
First draft of fixed fixmates program
Second draft of revised fixmates
Add code to disable proper pair check.
Polish by adding a little info to manual page, ensuring unmapped unpaired reads are treated the same as paired ones and adding details to how things work comment.
Fix assert > to >=.
Set the PAIRED flag once we have a pair
Fix edge case where last read in BAM is unpaired.
Fix compiler warning about \!
Fix accidently inverted flag check for unmapped
Add a few tests for fixmate
Add GPL header template.
Add brackets around bam_mating core unmapped check to avoid warning.
Fix edge case where pos = 1, caused by fact bam1_t is 0 based whilst sam text format is 1 based.
Correct flag check
Add MQ tags when doing fixmates.
Use STDIN_FILENO constant rather than fileno(stdin) and same for stderr in bam_mate.c.
Port to new htslib architecture
Make "CT" aux tag defined in bam_mate.c "ct" because it conflicts with existing defined CT tag.
Fix annoying memset warning and bug in md5.c
Fix error in bam.h comment
Add properly paired to stats and correct definition in flagstat
Replace bam2fq numbers with existing constants
Remove global variables from samtools view
Add ability to strip aux tags to samtools view
Add some more comments to tview
Reenable tview and port to htslib
Restore sample selection to tview and add a unit test for the code doing it.
Add a few comments to bam merging function
WIP on header merging
Add target id translation code and write pseudo code for building RG and PG translation tables
Convert PG and RG pseudo code to working code.
Further work on bam merge to fix header produced
Fix bugs picked up by unit testing.
More work on merging @RG and @PG tags into header.
Unit tests for merge
add skeleton code for PP processing
NULLify some freed pointers.
Unit test trans_tbl_init add test 5 for PG tags
Fix memory leaks and finalise @PG PP handling
Test @PG merging and PP handling
Integrate new header merging code into bam_sort main function
Clean up old dead code
Fix case where PG or RG tag is present on read but not in header.
Add test bams
Fix spaces to tabs
Eliminate compiler warnings in a cross-platform safe way.
Add unit test for bam_translate (WIP)
Fix edge case
Add unit test for tid translation
Add additional unit tests for bam_translate for PG and RG tags.
Adjust how merge handles duplicated PG and RG tags.
Add command line support for combining tags
Don't merge header into itself
Correct header length in test
Fix memory leak in trans_tbl_init
Enhance description of what we do
Add warning when merging causes coordinate sort to be lost
Reorder merge code so that BAM gets translated before it is inserted into heap.
Create slightly more sophisticated unit tests for merge
Convert merge reverse translation build to own function.
Ensure make only runs on make test
Add clock based randomness to merge and option to fix random seed.
Correct lost sort order detection in merge
Fix regex to pick out sequence ids
Add rtrans_build unit test stub
More work on rtrans_build unit test.
Fix position of bam_translate in merge read loop.
Deal with case where merged region does not exist in header of one of our input files.
hts_iter_t is not a pointer unlike it's predecessor
Add function to prettify header output by sorting it by defined order.
Instead of relying on NULL iter in merge use HTS_IDX_START
Ignore generated test files
In bam sort and merge change:
Fix merge unit tests under Linux
Initialise un-inited variable in test_bam_translate.
Revise merge header matching regex from spec
Make it easier to tell merge test phases apart
Apparently some programs put spaces into their @PG and @RG ID's.
Add option to vary level of verbosity.
Fix bug where wrong flag was being checked in header merge (merge rg vs merge pg)
Add PG tags to @RG lines testcases.
When merging instead of segfaulting when there is no index, return an error. Need to think of better ways to handle this.
Fix to use htslib commands.
Port bam_sort.c completely to new API.
Fix up tests for htslib architecture
Add -b option to merge to allow the specification of a list of files as alternative to putting them on the command line.
bam_merge: get rid of asprintf warnings
bam_merge tests: fix warnings
Mike Lin (1):
Fix control of compression level in bam_merge_core. The setting was ineffective due to a minor copy/paste error.
Nicholas Clarke (3):
Adds support for outputting stats over the full input size distribution.
Remove unusued 'total' functions.
Fixes an issue with -i0 involving truncation of insert sizes.
Petr Danecek (100):
Added BGZF indexing and reindexing capability to bgzip. Fixed -b seeking.
Added a test suite for samtools, currently faidx and bgzip are tested.
Added a test suite for samtools, currently faidx and bgzip are tested.
tview and bgzip: Check that the files are bgzipped, not gzipped.
This is a backup commit. Samtools mpileup seems to be working well in this version, but should be still considered experimental.
Merge branch 'with-htslib' of github.com:samtools/samtools into with-htslib
Added new forgotten file
bgzip: Do not overwrite input files when -b or -s are given
Moved bamcheck into "samtools stats"
Moved bamcheck into "samtools stats"
mpileup backup commit: New test annotation
Phony force target in Makefile
mpileup: Trial implementation of MWU CDF (rather than prob.)
New header file: samtools.h
mpileup: Fix in CDF version of MWU
Merge branch 'with-htslib' of github.com:samtools/samtools into with-htslib
mpileup: MWU CDF calculation in some cases returns value bigger than 1. Added a temporary check until this is resolved.
mpileup: fixed silly a typo in the previous commit
New test and updated VCF header samtools command string
MWU correction for ties
stats: Removed unused stats code (NMQ)
mpileup: Updated to the latest htslib API; disabled tie correction in MWU for now, as the results look suspicious
mpileup: Updated to htslib vcf module changes
Resolved merge conflicts
Merge branch 'develop' of github.com:samtools/samtools into develop
mpileup: Added -x option to disable overlap detection
Updated tests and recovered output previously disabled for debugging
Check return status of IO calls to prevent gcc 4.6.3 warnings
mpileup: Detect non-recoverable errors and exit with proper status
Merge branch 'develop' of github.com:samtools/samtools into develop
stats: Removed a too strict assert
Merge branch 'fix' into calling
Merge branch 'calling' into develop
stats: Fixed off-by-one error in GCD stats which overestimated GC content by 1 part in GCD bin size
Merge branch 'calling' into develop
Check return status of IO calls to prevent gcc 4.6.3 warnings
mpileup: Detect non-recoverable errors and exit with proper status
stats: Fixed off-by-one error in GCD stats which overestimated GC content by 1 part in GCD bin size
Merge branch 'develop' into calling
mpileup: Fix SGB numerical underflow; Output correct samtools version on output
mpileup: Added forgotten #include
mpileup: Prevent under/overflow of the SGB annotation
mpileup: Updated tests to reflect SGB change
mpileup: Allow up to five alleles (N,A,C,G,T)
New "flags" command plus moved filtering from htslib/pileup to BAM reading callbacks
On behalf of Peter Chines, test that filter mask replaces (not just adds to) default mask
mpileup: Disabled CDF version of MWU annotations and made it optional at compile time
Merge branch 'develop' into calling
Merge branch 'calling' into develop
plot-bamstats: Skip generation of empty GCD graphs
stats: Fix of mismmatch-per-cycle calculation in presence of hard-clipped reads
Moved khash_utils.h into htslib
Updated the khash_utils.h dependency
stats: realloc buffers in MPC calculation if necessary, unclipped length can be bigger seq_len
mpileup: Removed bcf_hdr_fmt_text() which is no longer necessary
Updated test
flags: Fixed a typo
mpileup: -q now takes effect also with -C
mpileup: Apply -Q switch also to MQ output
mpileup: Fixed broken IMF annotation
Added mpileup tests for CRAM
Make int size explicit for bcf_get_*_int calls
stats: More understandable output fields naming
Updated mpileup test to reflect change in overlap quals
view: Free the header once finished
merge,sort: Output BAM, not SAM. Build indexes
plot-bamstats: Fixes #183
Support for =X cigars in mpileup, exit on yet untreated cigars.
Free all memory in sparse_isize_free
stats: Support for =X cigars
Added expected outputs for stats tests
stats: Prevent nan on output
mpileup: Long options; Custom DP,DV,DP,DP4 format fields on output
Removed debugging exit in test.pl; Updated excl/incl long opts
mpileup opts: -1,2 now recognised, --ff,rf on popular demand back
mpileup opts: Added forgotten --ff
For your amusement, --ff goes with -2
mpileup: Long options
mpileup: Absolute INFO/QS to allow incremental calling
mpileup: support for BAM_CHARD_CLIP cigar
stats: Simplified usage of --GC-depth, reflen not required
stats: Check for zero-length cigars (e.g. 0D)
mpileup: Per-sample rather than cumulative QS. (experimental)
mpileup: Updated tests
Merge branch 'develop' into QS-vs-PL
mpileup: Reflect change in bcf_hdr_add_sample() usage
mpileup tests: Remove temporary hack, view -C -T now works
Updated calling section of samtools man page
mpileup: New optional FORMAT/DPR and INFO/DPR annotations
mpileup: Output symbolic <X> allele instead of VCF-incompatible X
mpileup: Support for cigar operator "P", resolves #243
mpileup: Do not crash on non-existent files, resolves #244
mpileup: Fix in DPR calculation - there can be
tview: Recover from incomplete fai files
mpileup: Support for cigar operation N
plot-bamstats: better support for plots of single-read bams
stats: Accept string flags with -f/F
plot-bamstats: Generate summary html page
plot-bamstats: Use 0x1 rather than 0x2 flag to detect paired-end
plot-bamstats: fixes in create_html and gz input
Rob Davies (36):
Adds *~ (emacs backup files) and core to .gitignore.
Adds tests for samtools view.
Merge branch 'develop' into develop_testing
Turns on CRAM region tests, now that CRAM indexing is supported.
Adds -L (BED file reading) tests.
Adds tests for the -t, -T and -B options.
Adds more region tests.
Rolls converting back to SAM into run_view_test
Adds CRAM conversion using the MD5 REF_CACHE.
Merge branch 'develop' into develop_testing
Strips out -x / -X tests as -X is deprecated and -x has been repurposed.
Adds more optional fields in test file, and more -R / -r checks.
Adds tests for the new -x tag stripping option.
Adds tests for currently undocumented -m and -Q options.
Adds some unaligned reads to the samtools view test file.
Minor changes to samtools view test output file names.
Adds tests for the -s (subsampling) and -@ (threads) options
Makes filter_sam filter @RG lines when filtering by read group.
Adds comments to explain how the samtools view testing functions work.
Changes *_compare functions to not call passed() or failed().
Removes dependency on gunzip
Merge branch 'develop' into develop_testing
Adds tests for 'samtools cat'
Makes -r and -R read group filtering options both use settings.rghash
Adds more optional tags to alignment lines.
Rewrite bed_read
Adds check to ensure bed_read worked, and exits non-zero if not.
Stops samtools view from writing unmapped reads with -L (BED file) option
Ensures non-zero exit if -r / -R options fail to work.
Limits -Q option (qual_scale) to sensible range 0 to 93.
Makes samtools view subsampling option more random.
Add tests for bam2fq.
Adds tests for samtools depad.
Adds expected fail and unexpected pass.
Add seq_cache_populate.pl
Add tests for making CRAM files using samtools view -t/-T
Sam Nicholls (17):
Add -b parameter to samtools merge manpage
Update samtools.1
Match style for FILE option
Alternate syntax for samtools merge.
Alternate syntax for samtools merge in stderr message
Clarify list is not a literal
Match samtools merge manpage and stderr syntax
Fix getline memory leak in test_bam_translate
Fix memory leak in test_rtrans_build
Fix memory leak in test_trans_tbl_init
Add missing fclose of orig_stderr to test_bam_translate
Fix getline memory leak in test_filter_header_rg
Fix getline missing fcloses in test_parse_args
Add missing frees to test_parse_args
Free char* in parsed_opts in test_parse_args
No need to set len=0 before getline
Free all allocated names from count_RG
Sendu Bala (1):
fixed spelling mistake
Shane McCarthy (5):
fall over if a bed file given as an option cannot be read
samtools flags: add documentation. print out decimal representation in addition to hexadecimal and string representation
Deprecate `-S`, `-D`, `-V` in favour of `-t DP,DV,SP`
some progress for mpileup documentation
add tests for samtools index with large chromosome
dbolser-ebi (1):
Added links to 'sister' projects.
pd3 (7):
Create README.md
Merge pull request #95 from wtsi-hgi/develop
Merge pull request #121 from sm15/feature/bam_flags_docs
Merge pull request #174 from mp15/stats
Merge pull request #179 from mp15/stats
Merge pull request #184 from wtsi-hgi/features/unbounded-is
Merge pull request #186 from wtsi-hgi/issues/warn-unusued-fn
peterjc (1):
Raise error if give @HD SO:coordinate to 'samtools fixmate'
pruzanov (2):
Fixed script for parsing BLAST output
Fixed a few bugs in blast2sam.pl script, added POD documentation
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