Commits

Breadcrumbs

History for

on1f2ad54

User selector

All users

Datepicker

All time

Commit History

Commits on Sep 2, 2016

• New bcftools/csq command, regidx overhaul and new %TBCSQ query format.

  Show description for 85e11e2
  pd3

  committed
  85e11e2

  Copy full SHA for 85e11e2

Commits on Aug 16, 2016

• roh bugfixes and speedup

  Show description for 6a191d4
  pd3

  committed
  6a191d4

  Copy full SHA for 6a191d4

Commits on Aug 5, 2016

• merge: support for fa ref in gVCF merging, N's used only if ref not available

  

  pd3

  authored and

  mcshane

  committed
  c416da7

  Copy full SHA for c416da7

• merge: use local version of regidx

  mcshane

  committed
  87bcd36

  Copy full SHA for 87bcd36

• bcftools merge overhaul from @pd3 fork

  Show description for 6d202ed
  mcshane

  committed
  6d202ed

  Copy full SHA for 6d202ed

• mpileup: changes -G/--exclude-RG to -G/--read-groups

  Show description for ce6ebb9
  

  pd3

  authored and

  mcshane

  committed
  ce6ebb9

  Copy full SHA for ce6ebb9

• rename sample.* to bam_sample.*

  mcshane

  committed
  c879699

  Copy full SHA for c879699

• regidx: extend regidx API

  Show description for ef6773a
  mcshane

  committed
  ef6773a

  Copy full SHA for ef6773a

• regidx: import regidx api from htslib into bcftools

  Show description for 2aacec6
  mcshane

  committed
  2aacec6

  Copy full SHA for 2aacec6

• mpileup: new -s and -S options to include only selected samples

  Show description for 93bd1a6
  mcshane

  committed
  93bd1a6

  Copy full SHA for 93bd1a6

• mpileup: add --gvcf output mode

  Show description for 27608e7
  mcshane

  committed
  27608e7

  Copy full SHA for 27608e7

• add mpileup command to bcftools

  Show description for eaf41c0
  mcshane

  committed
  eaf41c0

  Copy full SHA for eaf41c0

Commits on Aug 3, 2016

• gtcheck: improved cross-check mode

  Show description for 64d9e1b
  

  pd3

  authored and

  mcshane

  committed
  64d9e1b

  Copy full SHA for 64d9e1b

Commits on Aug 2, 2016

• stats: make the AF binning code reusable

  

  pd3

  authored and

  mcshane

  committed
  630bf99

  Copy full SHA for 630bf99

• index: add option to set the path for the index file (samtools#437)

  Show description for 764c4bb
  mcshane

  authored
  764c4bb

  Copy full SHA for 764c4bb

Commits on Apr 22, 2016

• Release 1.3.1: bug fixes, new GTisec plugin

  jmarshall

  committed
  0f1bc9d

  Copy full SHA for 0f1bc9d

Commits on Mar 16, 2016

• Mark error() as HTS_NORETURN

  Show description for 3eb4e8e
  jmarshall

  committed
  3eb4e8e

  Copy full SHA for 3eb4e8e

Commits on Jan 15, 2016

• concat: new --naive option for fast operations on large BCFs

  

  pd3

  authored and

  mcshane

  committed
  36036cf

  Copy full SHA for 36036cf

Commits on Dec 15, 2015

• Release 1.3: various new options, plugins, and bug fixes

  jmarshall

  committed
  d388dd1

  Copy full SHA for d388dd1

Commits on Nov 10, 2015

• Dynamically export bcftools symbols to plugins

  Show description for 2e5fda7
  jmarshall

  committed
  2e5fda7

  Copy full SHA for 2e5fda7

Commits on Oct 2, 2015

• Makefile: remove unnecessary "\"

  mcshane

  committed
  4923227

  Copy full SHA for 4923227

• add plugin to color shared chromosomal segments

  mcshane

  committed
  fe79a91

  Copy full SHA for fe79a91

Commits on Sep 2, 2015

• Merge new handling of ploidy (PR samtools#313)

  Show description for fcd451b
  jmarshall

  committed
  fcd451b

  Copy full SHA for fcd451b

Commits on Jul 28, 2015

• remove install dependency on asciidoc

  Show description for 0bde8e0
  mcshane

  committed
  0bde8e0

  Copy full SHA for 0bde8e0

Commits on Jul 6, 2015

• Fix polysomy dependencies [minor]

  jmarshall

  committed
  aea4cf9

  Copy full SHA for aea4cf9

Commits on Jun 13, 2015

• polysomy: new options, large rewrites at mostly unchanged performance

  Show description for 278cb33
  

  pd3

  authored and

  mcshane

  committed
  278cb33

  Copy full SHA for 278cb33

Commits on Mar 20, 2015

• Merge plugin installation (PR samtools#206)

  jmarshall

  committed
  70f0cec

  Copy full SHA for 70f0cec

• Update $BCFTOOLS_PLUGINS handling

  Show description for bea7d08
  jmarshall

  committed
  bea7d08

  Copy full SHA for bea7d08

Commits on Mar 16, 2015

• Apple's .dSYM debugging byproducts are directories

  jmarshall

  committed
  03faafd

  Copy full SHA for 03faafd

• [Makefile] Use user's CPPFLAGS/LDFLAGS/LIBS variables

  Show description for 54d6c82
  jmarshall

  committed
  54d6c82

  Copy full SHA for 54d6c82

Commits on Feb 5, 2015

• make install installs plugins

  Show description for 0ffc217
  wookietreiber

  committed
  0ffc217

  Copy full SHA for 0ffc217

Commits on Feb 2, 2015

• Release 1.2: new consensus command and annotate plugins, bug fixes

  jmarshall

  committed
  3529081

  Copy full SHA for 3529081

Commits on Jan 30, 2015

• Rename to LICENSE

  Show description for aeafbf4
  jmarshall

  committed
  aeafbf4

  Copy full SHA for aeafbf4

Commits on Jan 16, 2015

• New test-plugins makefile rule

  pd3

  committed
  1f79bbd

  Copy full SHA for 1f79bbd

Commits on Oct 15, 2014

• LICENSE renamed to COPYING

  pd3

  committed
  a2e5b56

  Copy full SHA for a2e5b56

Pagination

Previous

Next