2013-03-20 |
Petr Danecek | mpileup fix: Print error message and exit when no files... |
commit | commitdiff | tree | snapshot |
2013-03-18 |
Petr Danecek | bcftools: version bump |
commit | commitdiff | tree | snapshot |
2013-03-15 |
Petr Danecek | Version bump |
commit | commitdiff | tree | snapshot |
2013-03-15 |
Petr Danecek | Updated NEWS document |
commit | commitdiff | tree | snapshot |
2013-03-15 |
Petr Danecek | Merge remote branch 'pd3master/master' |
commit | commitdiff | tree | snapshot |
2013-03-15 |
Petr Danecek | Get rid of %ld-with-int64_t warning on Mac |
commit | commitdiff | tree | snapshot |
2013-03-15 |
Petr Danecek | Updated man pages |
commit | commitdiff | tree | snapshot |
2013-03-15 |
Petr Danecek | mpileup: New HWE, QBD, RPS annotations. Modified VDB... |
commit | commitdiff | tree | snapshot |
2013-03-12 |
Petr Danecek | Fixed brackets missing in the previous commit |
commit | commitdiff | tree | snapshot |
2013-03-12 |
Petr Danecek | Merge remote branch 'remotes/master/master' into fb... |
commit | commitdiff | tree | snapshot |
2013-03-12 |
Petr Danecek | backup commit |
commit | commitdiff | tree | snapshot |
2013-03-12 |
Petr Danecek | Merge branch 'master' of github.com:samtools/samtools |
commit | commitdiff | tree | snapshot |
2013-03-12 |
Petr Danecek | bcftools view: Exit with an error if the -l file cannot... |
commit | commitdiff | tree | snapshot |
2013-03-10 |
Heng Li | Merge pull request #30 from leecbaker/master |
commit | commitdiff | tree | snapshot |
2013-03-09 |
Lee Baker | Fix memory leaks: |
commit | commitdiff | tree | snapshot |
2013-03-07 |
Petr Danecek | backup commit |
commit | commitdiff | tree | snapshot |
2013-03-01 |
Petr Danecek | bcftools view: always output the header, even when... |
commit | commitdiff | tree | snapshot |
2013-02-27 |
Manuel Holtgrewe | Adding -f flag to samtools sort to give output name... |
commit | commitdiff | tree | snapshot |
2013-01-28 |
Petr Danecek | Merge remote branch 'remotes/pierre/master' into develop |
commit | commitdiff | tree | snapshot |
2013-01-25 |
lindenb | fix html |
commit | commitdiff | tree | snapshot |
2013-01-25 |
lindenb | cont |
commit | commitdiff | tree | snapshot |
2013-01-25 |
lindenb | works |
commit | commitdiff | tree | snapshot |
2013-01-25 |
lindenb | cont |
commit | commitdiff | tree | snapshot |
2013-01-25 |
lindenb | works with curses |
commit | commitdiff | tree | snapshot |
2013-01-25 |
Pierre Lindenbaum | cont |
commit | commitdiff | tree | snapshot |
2013-01-24 |
Pierre Lindenbaum | ... |
commit | commitdiff | tree | snapshot |
2013-01-07 |
Heng Li | dump log-likelihood |
commit | commitdiff | tree | snapshot |
2013-01-03 |
Petr Danecek | bamcheck: new stats, number of filtered vs raw sequences |
commit | commitdiff | tree | snapshot |
2012-12-13 |
Petr Danecek | Merge branch 'vsbuffalo-master' into develop |
commit | commitdiff | tree | snapshot |
2012-12-13 |
Vince Buffalo | fixed missing braces |
commit | commitdiff | tree | snapshot |
2012-12-13 |
Vince Buffalo | big fix: using samtools view file.bam gibberish returns... |
commit | commitdiff | tree | snapshot |
2012-12-12 |
Petr Danecek | mpileup: New --rf and --ff options for filtering reads |
commit | commitdiff | tree | snapshot |
2012-12-12 |
Petr Danecek | bamcheck: New stats - the number of QC failed reads... |
commit | commitdiff | tree | snapshot |
2012-12-12 |
Petr Danecek | bam2depth: Enabled reading the list of BAMs from a... |
commit | commitdiff | tree | snapshot |
2012-12-11 |
Petr Danecek | ksort.h: declared __ks_insertsort_##name as static... |
commit | commitdiff | tree | snapshot |
2012-12-03 |
Petr Danecek | bam_plcmd.c: more descriptive -b usage help message |
commit | commitdiff | tree | snapshot |
2012-12-03 |
Petr Danecek | bam_plcmd.c: added sanity check in read_file_list,... |
commit | commitdiff | tree | snapshot |
2012-12-03 |
Petr Danecek | bamcheck: New stats, number of pairs mapped to differen... |
commit | commitdiff | tree | snapshot |
2012-11-27 |
Petr Danecek | misc/Makefile, on behalf of ghuls: changed the order... |
commit | commitdiff | tree | snapshot |
2012-11-27 |
Petr Danecek | bamcheck: max quality value increased to 255 to handle... |
commit | commitdiff | tree | snapshot |
2012-11-22 |
Petr Danecek | bamcheck: Fixed a bug introduced by previous change... |
commit | commitdiff | tree | snapshot |
2012-11-15 |
Petr Danecek | Merge remote branch 'remotes/pd3master/master' into... |
commit | commitdiff | tree | snapshot |
2012-11-09 |
Petr Danecek | Drop empty bins from coverage distribution |
commit | commitdiff | tree | snapshot |
2012-11-09 |
Petr Danecek | Changed default reflen; more informative error message... |
commit | commitdiff | tree | snapshot |
2012-10-11 |
Petr Danecek | More user-friendly error output |
commit | commitdiff | tree | snapshot |
2012-10-10 |
Petr Danecek | Complain when BAM cannot be open. Severe bug fixed... |
commit | commitdiff | tree | snapshot |
2012-09-12 |
Petr Danecek | Merge remote branch 'remotes/pd3/master' |
commit | commitdiff | tree | snapshot |
2012-09-05 |
Petr Danecek | Fix in insertion cycle calculation of rev reads |
commit | commitdiff | tree | snapshot |
2012-09-05 |
Petr Danecek | GC-depth calculation now more robust to small GCD bin... |
commit | commitdiff | tree | snapshot |
2012-09-04 |
Petr Danecek | New --GC-depth option to bamcheck. Take into account... |
commit | commitdiff | tree | snapshot |
2012-08-21 |
Heng Li | Merge pull request #14 from peterjc/depad3 |
commit | commitdiff | tree | snapshot |
2012-08-17 |
peterjc | Fix 'samtools depad' seg-fault when MPOS/PNEXT given... |
commit | commitdiff | tree | snapshot |
2012-08-17 |
peterjc | Tweak order free things (avoids an 'samtools depad... |
commit | commitdiff | tree | snapshot |
2012-08-17 |
peterjc | First attempt at updating MPOS in 'samtools depad' |
commit | commitdiff | tree | snapshot |
2012-08-03 |
Heng Li | r580: bugfix - bam_aux_get() error given 'f' type |
commit | commitdiff | tree | snapshot |
2012-08-02 |
Petr Danecek | Use int64_t to prevent count overflow in view -c; on... |
commit | commitdiff | tree | snapshot |
2012-07-18 |
Petr Danecek | Fix in output of missing haploid genotypes |
commit | commitdiff | tree | snapshot |
2012-07-05 |
Petr Danecek | Allow filtering by read group or sample name in bamchec... |
commit | commitdiff | tree | snapshot |
2012-07-05 |
Petr Danecek | VCF annotations with and without -m and more robust... |
commit | commitdiff | tree | snapshot |
2012-07-03 |
Petr Danecek | Bug fixes |
commit | commitdiff | tree | snapshot |
2012-07-02 |
Petr Danecek | Alternative model for multiallelic and rare-variant... |
commit | commitdiff | tree | snapshot |
2012-06-27 |
Petr Danecek | New -p switch for increased sensititivy of indel-callin... |
commit | commitdiff | tree | snapshot |
2012-06-21 |
Petr Danecek | Merge branch 'master' of github.com:samtools/samtools |
commit | commitdiff | tree | snapshot |
2012-06-21 |
Petr Danecek | New -p option to start tview at desired position |
commit | commitdiff | tree | snapshot |
2012-06-19 |
Heng Li | r579: after merging Peter's depad changes |
commit | commitdiff | tree | snapshot |
2012-06-19 |
Heng Li | fixed a couple of minor compiling warnings |
commit | commitdiff | tree | snapshot |
2012-06-19 |
Heng Li | Merge pull request #11 from peterjc/depad2 |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Update @SQ lines during 'samtools depad' |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Calculate unpadded reference length, update BAM header... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | SAM/BAM input to 'samtools depad' not linked to FASTA... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Wording of error messages |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Catch missing reference error in faidx (avoids floating... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Check embedded reference against FASTA if given in... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Use FASTA file when no embedded reference in 'samtools... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Load FAI in 'samtools depad' (not used yet) |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Add reference FASTA file to 'samtools depad' command... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Support SAM or BAM input/output in 'samtools depad... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Minimal 'samtools depad' command line parsing (-? only... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Adding a usage function to 'samtools depad' following... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Add a tiny bit of help text to 'samtools depad' command. |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Revert one of my earlier changes - Heng was right,... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Fix buffer overflow in 'samtools depad' with CIGAR... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Fixed the next silly error on that line. |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Fix silly typo |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | More elegant solution to avoid superfluous leading... |
commit | commitdiff | tree | snapshot |
2012-06-19 |
peterjc | Refine logic for removing superfluous P ops (still... |
commit | commitdiff | tree | snapshot |
2012-06-12 |
Petr Danecek | Merge remote branch 'rq/getopt_mac' |
commit | commitdiff | tree | snapshot |
2012-06-12 |
peterjc | Fix missing declaration for getopt on Mac OS X |
commit | commitdiff | tree | snapshot |
2012-06-07 |
kortschak | Update bam1_core_t and bam1_t documentation |
commit | commitdiff | tree | snapshot |
2012-06-07 |
Petr Danecek | New -s option for multisample BAMs: include only reads... |
commit | commitdiff | tree | snapshot |
2012-05-30 |
Petr Danecek | Fixed errors introduced by the 8c15f916dabce475febdf508... |
commit | commitdiff | tree | snapshot |
2012-05-25 |
Petr Danecek | The -E switch to recalculate extended BAQ on the fly... |
commit | commitdiff | tree | snapshot |
2012-05-25 |
Petr Danecek | Fix to prevent long stretches of Ns to be mistaken... |
commit | commitdiff | tree | snapshot |
2012-05-18 |
Petr Danecek | Merge branch 'master' of github.com:samtools/samtools |
commit | commitdiff | tree | snapshot |
2012-05-18 |
Petr Danecek | Added -f, -F options. Count and plot indels per cycle... |
commit | commitdiff | tree | snapshot |
2012-05-17 |
Heng Li | change the default clevel to 1 for speed |
commit | commitdiff | tree | snapshot |
2012-05-17 |
Heng Li | added bamshuf from htslib |
commit | commitdiff | tree | snapshot |
2012-05-11 |
Heng Li | bugfix: bgzf-mt may write prematured output |
commit | commitdiff | tree | snapshot |
2012-05-05 |
Heng Li | added length threshold |
commit | commitdiff | tree | snapshot |
2012-05-03 |
Petr Danecek | Reverted to the previous behaviour, the unmapped reads... |
commit | commitdiff | tree | snapshot |
next |