[med-svn] [SCM] samtools annotated tag, 0.1.19, created. 0.1.19
Petr Danecek
pd3 at sanger.ac.uk
Sat Mar 30 09:17:14 UTC 2013
The annotated tag, 0.1.19 has been created
at 5f2c744c22c5c2d313ad73c594bdca244aa2dfa9 (tag)
tagging 44428cd6d2c6f24b7fe59e1333d883a5a1a11e12 (commit)
replaces st-final
tagged by Petr Danecek
on Tue Mar 19 08:07:16 2013 +0000
- Shortlog ------------------------------------------------------------
This release brings important bug fixes and improvements in the calling model (+version bump).
Heng Li (38):
updated with the latest bgzf library
preliminary implementation; not tested
multi-threading working on toy examples
bugfix in caching
use conditional variable
avoid wasting CPU time by the master thread
updated the alphanum comparison function
added mt comression to merge
added .gitignore
multi-threaded sorting
change the default block size in sorting
sorting also considers strand
name sorting checkes READ1 and READ2
Merge branch 'master' into mt
optionally surpress /[12] in bam2fq
control compression level at command line
a little more accurate mem estimate
change SO
move seqtk to a separate project
filter on query sequence length (not aln len)
Merge branch 'master' of github.com:samtools/samtools into mt
shrink bam1_t::m_data when sorting
compiling errors on some machines
Merge branch 'master' of github.com:samtools/samtools
updated to the latest kseq
change getline() to mygetline()
r572: added "bedcov" command
added length threshold
bugfix: bgzf-mt may write prematured output
added bamshuf from htslib
change the default clevel to 1 for speed
Merge pull request #11 from peterjc/depad2
fixed a couple of minor compiling warnings
r579: after merging Peter's depad changes
r580: bugfix - bam_aux_get() error given 'f' type
Merge pull request #14 from peterjc/depad3
dump log-likelihood
Merge pull request #30 from leecbaker/master
Lee Baker (1):
Fix memory leaks:
Manuel Holtgrewe (1):
Adding -f flag to samtools sort to give output name directly.
Petr Danecek (64):
Initial release of bamcheck and plot-bamcheck
Added rule for bamcheck creation
Compile cleanly from top-level Makefile. Check for out of bounds tids.
Temporary fix to prevent segfault in kpa_glocal
Merge remote branch 'main/master'
Removed glibc dependency (getline)
On behalf of Bradford Powell: fixed typo in VCF header, output DV not DP
Added check for out-of-bounds indels at the end of reads
Indexed access can be now combined with target regions. The number of mapped bases more accurate now with -t.
Resolved merge conflict
init_regions: check for non-matching sequence names
Reverted to the previous behaviour, the unmapped reads are not removed. Added -r switch for backward compatibility.
Added -f, -F options. Count and plot indels per cycle for each mate pair separately.
Merge branch 'master' of github.com:samtools/samtools
Fix to prevent long stretches of Ns to be mistaken for indels; Always output the most likely ALT allele
The -E switch to recalculate extended BAQ on the fly, ignoring existing BQs
Fixed errors introduced by the 8c15f916dabce475febdf508a9cc0c708c5a7747 commit.
New -s option for multisample BAMs: include only reads from a given sample in the display
Merge remote branch 'rq/getopt_mac'
New -p option to start tview at desired position
Merge branch 'master' of github.com:samtools/samtools
New -p switch for increased sensititivy of indel-calling. Here -m and -F are used per-sample which enables to detect rare indels in low-coverage bams. Experimental.
Alternative model for multiallelic and rare-variant calling. Proof-of-principle implementation.
Bug fixes
VCF annotations with and without -m and more robust rm_info
Allow filtering by read group or sample name in bamcheck. Bug fix in rm_info.
Fix in output of missing haploid genotypes
Use int64_t to prevent count overflow in view -c; on behalf of Joshua Randall: Set y2range in quals2.png plot
New --GC-depth option to bamcheck. Take into account not so frequent CIGAR codes. Fix in realloc_buffers. Prevent segfault with long command line options; Set xrange correctly in plot-bamcheck coverage.gp
GC-depth calculation now more robust to small GCD bin sizes
Fix in insertion cycle calculation of rev reads
Merge remote branch 'remotes/pd3/master'
Complain when BAM cannot be open. Severe bug fixed in -m haploid calling.
More user-friendly error output
Changed default reflen; more informative error message when GCD bin size too small or reflen too big
Drop empty bins from coverage distribution
Merge remote branch 'remotes/pd3master/master' into develop
bamcheck: Fixed a bug introduced by previous change igcd to uint: not a good idea to init with -1.
bamcheck: max quality value increased to 255 to handle missing qual field; pairs with IS=0 can still count as paired; output IS=0 stats as well
misc/Makefile, on behalf of ghuls: changed the order of bamcheck rules with -lz last
bamcheck: New stats, number of pairs mapped to different chromosomes
bam_plcmd.c: added sanity check in read_file_list, complain if file list is not a file list
bam_plcmd.c: more descriptive -b usage help message
ksort.h: declared __ks_insertsort_##name as static to compile with C99. (On behalf of Hanspeter Niederstrasser.)
bam2depth: Enabled reading the list of BAMs from a file list
bamcheck: New stats - the number of QC failed reads and non-primary alignments
mpileup: New --rf and --ff options for filtering reads
Merge branch 'vsbuffalo-master' into develop
bamcheck: new stats, number of filtered vs raw sequences
Merge remote branch 'remotes/pierre/master' into develop
bcftools view: always output the header, even when no other arguments are given
backup commit
bcftools view: Exit with an error if the -l file cannot be read
Merge branch 'master' of github.com:samtools/samtools
backup commit
Merge remote branch 'remotes/master/master' into fb-annots
Fixed brackets missing in the previous commit
mpileup: New HWE, QBD, RPS annotations. Modified VDB (beware: this version of VDB may be broken). Fix in indel calling: Ignore insertions with N's. Output contigs in the VCF header. New sam_header2tbl_n() API call.
Updated man pages
Get rid of %ld-with-int64_t warning on Mac
Merge remote branch 'pd3master/master'
Updated NEWS document
Version bump
bcftools: version bump
Pierre Lindenbaum (2):
...
cont
Vince Buffalo (2):
big fix: using samtools view file.bam gibberish returns alignments; iter not checked against kh_end
fixed missing braces
kortschak (1):
Update bam1_core_t and bam1_t documentation
lindenb (5):
works with curses
cont
works
cont
fix html
peterjc (23):
Fix missing declaration for getopt on Mac OS X
Refine logic for removing superfluous P ops (still testing ...)
More elegant solution to avoid superfluous leading P ops
Fix silly typo
Fixed the next silly error on that line.
Fix buffer overflow in 'samtools depad' with CIGAR D operators
Revert one of my earlier changes - Heng was right, CIGAR P not sensible in a padded reference
Add a tiny bit of help text to 'samtools depad' command.
Adding a usage function to 'samtools depad' following 'samtools view' style
Minimal 'samtools depad' command line parsing (-? only so far)
Support SAM or BAM input/output in 'samtools depad' (default still BAM -> BAM)
Add reference FASTA file to 'samtools depad' command line (not used yet)
Load FAI in 'samtools depad' (not used yet)
Use FASTA file when no embedded reference in 'samtools depad'
Check embedded reference against FASTA if given in 'samtools depad'
Catch missing reference error in faidx (avoids floating point exception)
Wording of error messages
SAM/BAM input to 'samtools depad' not linked to FASTA reference
Calculate unpadded reference length, update BAM header (SAM header pending)
Update @SQ lines during 'samtools depad'
First attempt at updating MPOS in 'samtools depad'
Tweak order free things (avoids an 'samtools depad' seg fault on error)
Fix 'samtools depad' seg-fault when MPOS/PNEXT given but MRNM/RNEXT is not
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Processing of sequence alignments in SAM and BAM formats.
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