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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

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• RoH bugfix: Transition probabilities must scale to 1

  

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  authored and

  mcshane

  committed
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• The HMM structure becomes opaque for future flexibility

  

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  authored and

  mcshane

  committed
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Commits on Jan 16, 2015

• Replaced ato[if] with strto[lf] to recognise user errors

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Commits on Jan 15, 2015

• cnv improvements:

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Commits on Oct 21, 2014

• Do not use 0x80 & co for missing alleles

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  committed
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Commits on Oct 20, 2014

• use new htslib file type detection and error reporting API

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  committed
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Commits on Aug 26, 2014

• roh: reset counts with next chromosome

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  committed
  b0ac420

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• Small improvemens and fixes in roh

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  committed
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• Merged with develop

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Commits on Aug 14, 2014

• Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT

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  committed
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Commits on Aug 13, 2014

• Reformat license text

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Commits on Aug 11, 2014

• Write out description and author in each source file header

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  committed
  28e88c8

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Commits on Jul 29, 2014

• roh: Allow PLs bigger than 255

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  committed
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Commits on Jul 3, 2014

• roh bug fix: Use nsites, not args->nsites

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  committed
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Commits on Jul 1, 2014

• roh: -M for constant recombination rate; support for

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Commits on Jun 27, 2014

• RoH: Updated docs, more intuitive variable naming

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  committed
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Commits on Jun 23, 2014

• RoH rewritten for greater flexibility, experimental

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  committed
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Commits on May 7, 2014

• Fixed long options with no argument

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Commits on Apr 1, 2014

• Improved descriptions of --samples[-file] option

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• Added copyright notice

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  committed
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• Added -S,-R,-T options

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  committed
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Commits on Feb 21, 2014

• usage displays for .vcf.gz only

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  committed
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• consistency and cosmetic updates to help messages

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Commits on Feb 17, 2014

• Make int size explicit for bcf_get_*_int calls

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  committed
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Commits on Feb 13, 2014

• roh: Use fixed crossover LK if genmap not given

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  committed
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Commits on Feb 12, 2014

• roh: New -F option

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  committed
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Commits on Jan 30, 2014

• roh: Init HMM with new chromosome

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  committed
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• roh: fixed genetic map and -G handling

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Commits on Jan 21, 2014

• roh: Added forgotten break

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• roh: Fixed a typo

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  committed
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• roh: -e to calculate AF on the fly

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  committed
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• roh: Throw an error if PL not present and -G not given

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  committed
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Commits on Jan 15, 2014

• roh: New -I option; Fix in chr switching; Skip chrs w/o genmap

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• roh: New -b option, fixed PL-based pdg initialization

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  committed
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