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Commits on Mar 28, 2024

• Add short option -W for --write-index.

  Show description for ca95dfe
  

  jkbonfield

  authored and

  pd3

  committed
  ca95dfe

Commits on Feb 17, 2022

• Add --regions/--targets-overlap pos|record|variant mnemonic options

  Show description for f794342
  jmarshall

  committed
  f794342

Commits on Jan 31, 2022

• Fix an API error, see samtools#1647 for discussion

  pd3

  committed
  ce4cd89

Commits on Sep 27, 2021

• Fixes the python plotting routines.

  

  Sebastian Schmeier

  authored and

  pd3

  committed
  f438086

Commits on Sep 7, 2021

• Finer control of --regions vs --targets overlap

  Show description for 0d04159
  pd3

  committed
  0d04159

Commits on Feb 20, 2020

• Use #include <assert.h> in source files that use assert()

  Show description for 42d777e
  jmarshall

  committed
  42d777e

Commits on Sep 9, 2019

• Prepare for 64-bit positions

  Show description for aec5177
  daviesrob

  committed
  aec5177

Commits on Apr 15, 2019

• Improve error messages. Resolves samtools#951 and samtools#925

  pd3

  committed
  be4494b

Commits on Sep 24, 2018

• Minor fix: add missing test file; add missing long options. Fixes samtools#890

  pd3

  committed
  2dd4ea5

Commits on Jul 19, 2018

• Check return status of all *write() and *close() calls

  pd3

  committed
  69711c9

Commits on Feb 7, 2018

• Update copyright years

  pd3

  committed
  a3839ab

• Replace python open(...,'rb') with open(...,'r')

  Show description for 7261871
  pd3

  committed
  7261871

Commits on Jul 26, 2017

• Fix bug in mkdir_p which caused

  Show description for 69e2785
  pd3

  committed
  69e2785

Commits on Aug 25, 2016

• Make the HMM API more convenient; Fix eprob overlap bug in vcfroh

  pd3

  committed
  a54f604

Commits on Aug 24, 2016

• Extended HMM API

  pd3

  committed
  75eb071

Commits on Jun 21, 2016

• cnv: add params estimated by -O to the summary cnv output

  

  pd3

  authored and

  mcshane

  committed
  be8b378

Commits on Oct 22, 2015

• Reduce memory consumption in cnv plotting script

  

  pd3

  authored and

  mcshane

  committed
  e325cd0

• CNV output include number of sites/hets in regions

  

  pd3

  authored and

  mcshane

  committed
  2fc54de

• cnv: New -k option, fixed non-functional parsing of -dfloat,float

  

  pd3

  authored and

  mcshane

  committed
  983067a

Commits on Jul 7, 2015

• cnv: Prior on CN2; changed the default -P to be more strict (0.5)

  

  pd3

  authored and

  mcshane

  committed
  d3f9fe4

• cnv: Update to the modified HMM API

  

  pd3

  authored and

  mcshane

  committed
  2b50604

• cnv -O: Increase robustness by smoothing HMM lks before updating the mean

  

  pd3

  authored and

  mcshane

  committed
  d2b012f

• Updated cnv command:

  Show description for ddc0bef
  

  pd3

  authored and

  mcshane

  committed
  ddc0bef

Commits on Jul 6, 2015

• New bcftools roh --AF-dflt option; changed -a,-H defaults; fixed a bug in -e -

  

  pd3

  authored and

  mcshane

  committed
  3ba5f38

• RoH bugfix: Transition probabilities must scale to 1

  

  pd3

  authored and

  mcshane

  committed
  f506244

• The HMM structure becomes opaque for future flexibility

  

  pd3

  authored and

  mcshane

  committed
  8fdd498

Commits on Jan 15, 2015

• cnv improvements:

  Show description for f0922b6
  pd3

  committed
  f0922b6

Commits on Dec 16, 2014

• Modified CNV transition matrix and more:

  Show description for 7c13d5b
  pd3

  committed
  7c13d5b

Commits on Nov 28, 2014

• cnv: Test for NaN LRR values

  pd3

  committed
  1681154

Commits on Nov 25, 2014

• cnv fix: CN4 peaks centered differently than CN3 peaks!

  pd3

  committed
  2b236ca

Commits on Oct 20, 2014

• use new htslib file type detection and error reporting API

  pd3

  committed
  611c7e3

Commits on Sep 4, 2014

• Improved polysomy evaluation; changed cnv -i default value

  Show description for 7270394
  pd3

  committed
  7270394

Commits on Sep 3, 2014

• cnv: Allow file streams

  pd3

  committed
  eb57b8a

Commits on Sep 2, 2014

• New cnv command for copy number variation

  pd3

  committed
  93f17fe

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