[med-svn] [htslib] annotated tag 0.2.0-rc8 created (now 9cd630f)
Charles Plessy
plessy at moszumanska.debian.org
Mon Aug 18 12:06:20 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to annotated tag 0.2.0-rc8
in repository htslib.
at 9cd630f (tag)
tagging 8deb11d96daffee0f3b1c358377b05898129a304 (commit)
replaces 0.2.0-rc7
tagged by John Marshall
on Thu May 8 13:20:26 2014 +0100
- Log -----------------------------------------------------------------
Test release RC8
Heng Li (35):
Create trunk copy
initial source code. It is BUGGY!
bgzip is more like gzip in its command-line interface
* tabix-0.0.0-1 (r500) * apparently working
* tabix-0.0.0-2 (r501) * accelerate ti_readline()
* tabix-0.0.0-3 (r502) * support meta lines (not tested) * I am going to make the index file in the BGZF format
* tabix-0.0.0-4 (r503) * index files are bgzf compressed
* tabix-0.0.0-5 (r504) * fixed a critical bug in fetching data (a typo in fact) * support SAM (tested on ex1.sam) and VCF (not tested) * improve the command-line interface
documentation
Release tabix-0.1.0
Release tabix-0.1.1
* tabix-0.1.3 (r543) * fixed another off-by-one bug
removed a line of debugging code
* added the format specification * fixed a typo in bgzip
* tabix-0.1.3-2 (r555) * do not overwrite index file by default * a little code cleanup
* tabix-0.1.3-3 (r556) * fixed a small memory leak in knetfile * fixed a minor bug for remote downloading
Release tabix-0.1.4 (r559)
* Release tabix-0.1.5 (r560) * Improve seeking efficiency. Index file needs to be rebuilt.
If nothing bad happens, this will become 0.1.6
Release tabix-0.1.6
* improved C/Perl APIs * added test for Perl * added an tiny example
Release tabix-0.2.0
Release tabix-0.2.1
Release tabix-0.2.2
fixed a bug in C/Java when n_off == 0
patches by Peter Chines
Release tabix-0.2.3
BED support
update to the latest bgzf.*
fixed two bugs due to recent changes
update version number
Release tabix-0.2.4 (r949)
Release tabix-0.2.5 (r964)
updated BGZF
-C to output lines not overlapping BED
James Bonfield (4):
Bug fix to CRAM indexing and index usage.
Fixed two small memory leaks.
Revert one of the previous memory leaks as it breaks multi-threading.
Better fix for container memory leak.
John Marshall (22):
Use htslib's bgzf.h, faidx.h, and razf.h
Merge tabix and samtools bgzip.c and tabix.c
Merge branch 'bcftools+calling' into develop
Make hfile.h part of the public API
Add MIT/Expat license boilerplate
Define __attribute__ macros in a new (semi-public) header
Propagate error codes for CRAM_OPT_RANGE
Construct HTS_IDX_REST and HTS_IDX_NONE iterators without an index
Merge bam_dup1() addition (PR #80)
Silence -Wstrict-prototypes warnings
Merge bgzip.c and tabix.c/.1 history from github.com/samtools/tabix
Fix bgzip and tabix dependencies and link commands
Exit statuses are non-negative
Merge branch 'bcftools+calling' into develop
Silence -Wstrict-prototypes warning
Check sam_open() and sam_close() return values
Return "" from bam_flag2str(0) rather than NULL
Merge CRAM indexing bug fixes (PR #85)
Add hts_set_threads() file I/O threading API
Fix bgzf_write() and bgzf_flush_try() error handling
Fix bam_write1() error handling
Merge branch 'bcftools+calling' into develop
Joël Spaltenstein (1):
Fixed comment typo
Martin O. Pollard (2):
Reinstate bam_header_dup as bam_hdr_dup
Fix typo in comment
Martin Pollard (1):
Migrate documentation from samtools bam.h to sam.h and add a few more items
Mauricio Carneiro (1):
Add duplication function for the bam1_t interface
On behalf of Bob Handsaker (1):
Change copyright notices now that MIT has approved open source distribution.
Petr Danecek (51):
Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
Added the -l option for listing chromosomes
Fix in src/dst file detection and slight change of behaviour
The behaviour changed slightly to mimic gzip. Detect if std descriptors are connected to the terminal.
Complain about not-bgzipped files and check for noncontinuous chromosome blocks
Fix: Exit with an error rather than segfault when index is not present and region is queried
Added -h option to print header lines
Disable "unknown target name or minus interval" warning.
Prevent the common user mistake and check the timestamps of the vcf and index file
Fix: Complain only when VCF is newer, not newer or same mtime
New -r (reheader) option for efficient header replacement.
Querying remote files required -f option on some systems
Added option for printing header lines only
Guess the filetype from the file extension when -p not given
Assume GFF format when the file type cannot be guessed, as in the previous version
Even better, do this only for reading
Fix: allow custom formats
More informative error message about missing or out-of-date tabix index
Fix: do not drop first record with both -B and -h
bgzip now compiles
Added BGZF indexing and reindexing capability to bgzip. Fixed -b seeking.
tview and bgzip: Check that the files are bgzipped, not gzipped.
bgzip: Do not overwrite input files when -b or -s are given
Check return status of IO calls to prevent gcc 4.6.3 warnings
Initial version of bgzip and tabix with htslib.
synced_reader: Init position correctly
Merge branch 'develop' into bcftools+calling
Merge branch 'develop' into bcftools+calling
hts_idx: fixed indexing of NO_COOR blocks
This resolves #49
vcf: Propagate error in bcf_hdr_append
Fixed off-by-one in bcf_get_format_values
Propagate error from bcf_hdr_printf
hts_readlist modifed to explicitly indicate file name vs list
Support for =X cigars in mpileup overlaps.
faidx: Set error status if unknown seq is queried
bcf_hdr_subset: To allow sanity checks, mark missing samples
bcf_sr_seek to seek to start with seq=NULL
bcf_remove_alleles: Fix indexing range for Number=A alleles
Fixed BCF output after bcf1_sync_alleles, simplified
bcf_remove_alleles to work with BCF output
Added bgzip and tabix
.gitignore tabix and bgzip
bcf_subset: Reset n_fmt fields when all samples are dropped
synced_reader: Regions operate on two as well as three columns again
bcf1_sync: Update rlen for new records as well
bcf_write: sanity check the number of samples, resolves #55
vcf_parse: Detect missing INFO values in vectors
Merge branch 'develop' into bcftools+calling
For bcftools to work with CSI indexes up to 2^31-1
New bcf_hdr_[sg]et_version API; bcf_hdr_subset preserves VCF version
Shane McCarthy (1):
make sure we have found values for AC _and_ AN before using
pd3 (2):
Merge pull request #79 from spalte/comment_typo
Merge pull request #82 from sm15/feature/bcf_calc_ac_bugfix
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