| 2013-03-15 |
Petr Danecek | Merge remote branch 'pd3master/master'
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commit | commitdiff | tree |
| 2013-03-15 |
Petr Danecek | Get rid of %ld-with-int64_t warning on Mac
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commit | commitdiff | tree |
| 2013-03-15 |
Petr Danecek | Updated man pages
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commit | commitdiff | tree |
| 2013-03-15 |
Petr Danecek | mpileup: New HWE, QBD, RPS annotations. Modified VDB...
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commit | commitdiff | tree |
| 2013-03-12 |
Petr Danecek | Fixed brackets missing in the previous commit
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commit | commitdiff | tree |
| 2013-03-12 |
Petr Danecek | Merge remote branch 'remotes/master/master' into fb...
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commit | commitdiff | tree |
| 2013-03-12 |
Petr Danecek | backup commit
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commit | commitdiff | tree |
| 2013-03-12 |
Petr Danecek | Merge branch 'master' of github.com:samtools/samtools
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commit | commitdiff | tree |
| 2013-03-12 |
Petr Danecek | bcftools view: Exit with an error if the -l file cannot...
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commit | commitdiff | tree |
| 2013-03-07 |
Petr Danecek | backup commit
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commit | commitdiff | tree |
| 2013-03-01 |
Petr Danecek | bcftools view: always output the header, even when...
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commit | commitdiff | tree |
| 2013-01-28 |
Petr Danecek | Merge remote branch 'remotes/pierre/master' into develop
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commit | commitdiff | tree |
| 2013-01-03 |
Petr Danecek | bamcheck: new stats, number of filtered vs raw sequences
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commit | commitdiff | tree |
| 2012-12-13 |
Petr Danecek | Merge branch 'vsbuffalo-master' into develop
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commit | commitdiff | tree |
| 2012-12-12 |
Petr Danecek | mpileup: New --rf and --ff options for filtering reads
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commit | commitdiff | tree |
| 2012-12-12 |
Petr Danecek | bamcheck: New stats - the number of QC failed reads...
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commit | commitdiff | tree |
| 2012-12-12 |
Petr Danecek | bam2depth: Enabled reading the list of BAMs from a...
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commit | commitdiff | tree |
| 2012-12-11 |
Petr Danecek | ksort.h: declared __ks_insertsort_##name as static...
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commit | commitdiff | tree |
| 2012-12-03 |
Petr Danecek | bam_plcmd.c: more descriptive -b usage help message
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commit | commitdiff | tree |
| 2012-12-03 |
Petr Danecek | bam_plcmd.c: added sanity check in read_file_list,...
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commit | commitdiff | tree |
| 2012-12-03 |
Petr Danecek | bamcheck: New stats, number of pairs mapped to different...
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commit | commitdiff | tree |
| 2012-11-27 |
Petr Danecek | misc/Makefile, on behalf of ghuls: changed the order...
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commit | commitdiff | tree |
| 2012-11-27 |
Petr Danecek | bamcheck: max quality value increased to 255 to handle...
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commit | commitdiff | tree |
| 2012-11-22 |
Petr Danecek | bamcheck: Fixed a bug introduced by previous change...
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commit | commitdiff | tree |
| 2012-11-15 |
Petr Danecek | Merge remote branch 'remotes/pd3master/master' into...
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commit | commitdiff | tree |
| 2012-11-09 |
Petr Danecek | Drop empty bins from coverage distribution
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commit | commitdiff | tree |
| 2012-11-09 |
Petr Danecek | Changed default reflen; more informative error message...
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commit | commitdiff | tree |
| 2012-10-11 |
Petr Danecek | More user-friendly error output
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commit | commitdiff | tree |
| 2012-10-10 |
Petr Danecek | Complain when BAM cannot be open. Severe bug fixed...
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commit | commitdiff | tree |
| 2012-09-12 |
Petr Danecek | Merge remote branch 'remotes/pd3/master'
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commit | commitdiff | tree |
| 2012-09-05 |
Petr Danecek | Fix in insertion cycle calculation of rev reads
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commit | commitdiff | tree |
| 2012-09-05 |
Petr Danecek | GC-depth calculation now more robust to small GCD bin...
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commit | commitdiff | tree |
| 2012-09-04 |
Petr Danecek | New --GC-depth option to bamcheck. Take into account...
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commit | commitdiff | tree |
| 2012-08-02 |
Petr Danecek | Use int64_t to prevent count overflow in view -c; on...
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commit | commitdiff | tree |
| 2012-07-18 |
Petr Danecek | Fix in output of missing haploid genotypes
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commit | commitdiff | tree |
| 2012-07-05 |
Petr Danecek | Allow filtering by read group or sample name in bamcheck...
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commit | commitdiff | tree |
| 2012-07-05 |
Petr Danecek | VCF annotations with and without -m and more robust...
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commit | commitdiff | tree |
| 2012-07-03 |
Petr Danecek | Bug fixes
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commit | commitdiff | tree |
| 2012-07-02 |
Petr Danecek | Alternative model for multiallelic and rare-variant...
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commit | commitdiff | tree |
| 2012-06-27 |
Petr Danecek | New -p switch for increased sensititivy of indel-calling...
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commit | commitdiff | tree |
| 2012-06-21 |
Petr Danecek | Merge branch 'master' of github.com:samtools/samtools
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commit | commitdiff | tree |
| 2012-06-21 |
Petr Danecek | New -p option to start tview at desired position
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commit | commitdiff | tree |
| 2012-06-12 |
Petr Danecek | Merge remote branch 'rq/getopt_mac'
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commit | commitdiff | tree |
| 2012-06-07 |
Petr Danecek | New -s option for multisample BAMs: include only reads...
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commit | commitdiff | tree |
| 2012-05-30 |
Petr Danecek | Fixed errors introduced by the 8c15f916dabce475febdf508a9cc0...
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commit | commitdiff | tree |
| 2012-05-25 |
Petr Danecek | The -E switch to recalculate extended BAQ on the fly...
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commit | commitdiff | tree |
| 2012-05-25 |
Petr Danecek | Fix to prevent long stretches of Ns to be mistaken...
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commit | commitdiff | tree |
| 2012-05-18 |
Petr Danecek | Merge branch 'master' of github.com:samtools/samtools
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commit | commitdiff | tree |
| 2012-05-18 |
Petr Danecek | Added -f, -F options. Count and plot indels per cycle...
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commit | commitdiff | tree |
| 2012-05-03 |
Petr Danecek | Reverted to the previous behaviour, the unmapped reads...
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commit | commitdiff | tree |
| 2012-04-24 |
Petr Danecek | init_regions: check for non-matching sequence names
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commit | commitdiff | tree |
| 2012-04-23 |
Petr Danecek | Resolved merge conflict
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commit | commitdiff | tree |
| 2012-04-23 |
Petr Danecek | Indexed access can be now combined with target regions...
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commit | commitdiff | tree |
| 2012-04-12 |
Petr Danecek | Added check for out-of-bounds indels at the end of...
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commit | commitdiff | tree |
| 2012-04-12 |
Petr Danecek | On behalf of Bradford Powell: fixed typo in VCF header...
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commit | commitdiff | tree |
| 2012-04-04 |
Petr Danecek | Removed glibc dependency (getline)
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commit | commitdiff | tree |
| 2012-04-04 |
Petr Danecek | Merge remote branch 'main/master'
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commit | commitdiff | tree |
| 2012-04-02 |
Petr Danecek | Temporary fix to prevent segfault in kpa_glocal
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commit | commitdiff | tree |
| 2012-03-29 |
Petr Danecek | Compile cleanly from top-level Makefile. Check for...
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commit | commitdiff | tree |
| 2012-03-28 |
Petr Danecek | Added rule for bamcheck creation
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commit | commitdiff | tree |
| 2012-03-27 |
Petr Danecek | Initial release of bamcheck and plot-bamcheck
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commit | commitdiff | tree |
| 2011-02-03 |
Petr Danecek | Prevent division by zero
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commit | commitdiff | tree |
| 2011-01-19 |
Petr Danecek | Skip sites with unknown ref
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commit | commitdiff | tree |
| 2011-01-04 |
Petr Danecek | Fixed a typo in read_samples
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commit | commitdiff | tree |
| 2010-12-14 |
Petr Danecek | Fixed the VCF header to pass validation
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commit | commitdiff | tree |
| 2010-11-02 |
Petr Danecek | Added -b option: read file names from a file
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commit | commitdiff | tree |
| 2010-10-05 |
Petr Danecek | Convert VCF output of "bcftools view -bgcv" to a valid...
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commit | commitdiff | tree |
| 2010-06-11 |
Petr Danecek | Initial release on behalf of Aylwyn Scally
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commit | commitdiff | tree |
| 2010-05-07 |
Petr Danecek | Added a note about the indels coordinates
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commit | commitdiff | tree |
| 2010-04-23 |
Petr Danecek | Added the possibility to print or not to print the...
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commit | commitdiff | tree |
| 2010-04-15 |
Petr Danecek | More descriptive message for space separated tags
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commit | commitdiff | tree |
| 2010-04-14 |
Petr Danecek | Speedup with -i, no need to query the reference all...
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commit | commitdiff | tree |
| 2010-03-15 |
Petr Danecek | Fixed the order of sequences in the header
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commit | commitdiff | tree |
| 2010-03-04 |
Petr Danecek | Added possibility to select indels only and fixed a...
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commit | commitdiff | tree |
| 2010-02-26 |
Petr Danecek | Improved efficiency of header parsing
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commit | commitdiff | tree |
| 2010-02-17 |
Petr Danecek | Fixed filtering of SNPs near indels. Added min indel...
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commit | commitdiff | tree |
| 2010-02-12 |
Petr Danecek | Print an error for pileups in simple format
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commit | commitdiff | tree |
| 2010-02-09 |
Petr Danecek | Added possibility to specify a custom column title...
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commit | commitdiff | tree |
| 2010-02-09 |
Petr Danecek | Added the -d option to limit maximum depth for indels.
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commit | commitdiff | tree |
| 2010-02-03 |
Petr Danecek | Added VCF header
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commit | commitdiff | tree |
| 2009-12-11 |
Petr Danecek | Fixed a bug in knet_seek
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commit | commitdiff | tree |
| 2009-12-11 |
Petr Danecek | Small fix in VCF format: dot for the empty INFO field
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commit | commitdiff | tree |
| 2009-12-11 |
Petr Danecek | Allow tabs in the CO header field
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commit | commitdiff | tree |
| 2009-10-24 |
Petr Danecek | Added sam_header_line_free call for sam_header_parse2
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commit | commitdiff | tree |
| 2009-10-23 |
Petr Danecek | Now possible to merge multiple HeaderDict dictionaries
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commit | commitdiff | tree |
| 2009-10-22 |
Petr Danecek | (no commit message)
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commit | commitdiff | tree |
| 2009-10-22 |
Petr Danecek | (no commit message)
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commit | commitdiff | tree |
| 2009-10-09 |
Petr Danecek | Added the sam2vcf.pl script.
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commit | commitdiff | tree |
| 2009-10-08 |
Petr Danecek | Removed the offending knet_seek message.
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commit | commitdiff | tree |
| 2009-10-06 |
Petr Danecek | Bug fix - faidx on RAZF compressed files now working.
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commit | commitdiff | tree |
| 2009-09-28 |
Petr Danecek | Changed the mode for newly created files to 0666. This...
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commit | commitdiff | tree |
| 2009-09-16 |
Petr Danecek | A bug fix, "samtools view" is now working again.
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commit | commitdiff | tree |
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