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Commits on Sep 8, 2017

• Same as 8b53f1e but done differently

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  pd3

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Commits on Sep 7, 2017

• Support multi-sample files, in addition to multiple single-sample files

  pd3

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  8b53f1e

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Commits on Aug 29, 2017

• Make plot-vcfstats python3 compatible, resolves samtools#666

  pd3

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Commits on Jul 12, 2017

• plot-vcfstats: exit 0 when called with -h

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Commits on Jul 10, 2017

• Python3 fix for plot-vcfstats

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Commits on May 31, 2017

• Fixes and improvements in plot-roh.py

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  pd3

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Commits on May 26, 2017

• Open stats file in text mode, not binary. Fixes samtools#618

  pd3

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Commits on May 19, 2017

• New options for the ROH plotting script

  pd3

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Commits on Apr 18, 2017

• Change syntax for python2,3 compatibility. Fixes samtools#593

  pd3

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Commits on Apr 9, 2017

• Add two helper scripts run-roh.pl and plot-roh.py,

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Commits on Apr 7, 2017

• Move all helpler scripts to misc/ subdirectory

  pd3

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Commits on Aug 20, 2013

• Updated tests, cleaned the code to compile with the most recent HTSlib version.

  pd3

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Commits on Jul 12, 2013

• vcfcheck: re-enabled stats by QUAL

  pd3

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Commits on Jun 24, 2013

• vcffilter: Change in neighbourhood function in SOM training, seems more robust with respect to random seed

  pd3

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Commits on Jun 19, 2013

• vcfcheck: Fixed a bug in initialization of frame-shift calculation; More detailed FS output

  pd3

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Commits on Jun 12, 2013

• plot-vcfcheck: Produce the overlap by AF graphs

  pd3

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Commits on Jun 6, 2013

• vcfcheck: Changed output format of Ts/Tv

  pd3

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• vcffilter &friends: Filtering of indels now supported. Changes in vcfcheck, plot-vcfcheck and vcfquery to reflect that. More changes and fixes to come, but this version seems stable and fully funct…

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  pd3

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Commits on May 22, 2013

• vcfcheck: More readable output, replace "-" by "<STDIN>" when reading from standard input

  pd3

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Commits on May 16, 2013

• vcfcheck: create additional ts/tv stats which counts 1st alternate allele only

  pd3

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Commits on Mar 12, 2013

• do not round per-sample average depths to integer values

  mcshane

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Commits on Jan 16, 2013

• plot-vcfcheck: Escape all underscores summary.tex

  pd3

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• plot-vcfcheck: Prevent division by zero in FS merging

  pd3

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Commits on Dec 6, 2012

• plot-vcfcheck: zoomed y-range for ts/tv by sample graph

  pd3

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Commits on Nov 29, 2012

• Merge remote branch 'remotes/pd3master/master' into develop

  pd3

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• plot-vcfcheck: Fix in merging per-sample average depth - average, not sum

  pd3

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Commits on Nov 28, 2012

• plot-vcfcheck: Added missing legend into SNP/indel counts by AF graphs

  pd3

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Commits on Nov 23, 2012

• plot-vcfcheck: new -s switch; several new graphs and table values

  pd3

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Commits on Nov 19, 2012

• plot-vcfcheck: -T option to set PDF title; minor improvements in various plots

  pd3

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Commits on Nov 15, 2012

• plot-vcfcheck: removed forgotten debugging comments; merge of allelic r2 column in GCsAF

  pd3

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• plot-vcfcheck: fixed forgotten .pdf extension string

  pd3

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• vcfcheck: New stats and graph, allelic r2 by AF

  pd3

  committed
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Commits on Nov 13, 2012

• plot-vcfcheck: fixex merging of per-sample stats

  pd3

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• plot-vcfcheck: New --rasterize option for fast PDF rendering

  pd3

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Commits on Nov 5, 2012

• Sanity check allow output from both vcfcheck and plot-vcfcheck -m

  pd3

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