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Commits on Jun 20, 2013

• avoid division by zero error

  mcshane

  committed
  1e1b729

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Commits on Jun 19, 2013

• Summary commit of several important changes, new features and bugfixes in vcffilter, vcfcheck, vcfnorm and other tools.

  pd3

  committed
  063170b

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Commits on Jun 12, 2013

• plot-vcfcheck: Produce the overlap by AF graphs

  pd3

  committed
  c0184e3

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Commits on Jun 6, 2013

• vcfcheck: Changed output format of Ts/Tv

  pd3

  committed
  41d7218

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• vcffilter now supports indels, new indel metrics in vcfcheck

  pd3

  committed
  38e4758

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Commits on May 16, 2013

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

  pd3

  committed
  ad4a57b

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Commits on Mar 26, 2013

• pull in change from master: do not round per-sample average depth to integer

  mcshane

  committed
  58ec36c

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Commits on Jan 16, 2013

• Escape all underscores summary.tex

  pd3

  committed
  02f3b74

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• Prevent division by zero in FS merging

  pd3

  committed
  f4314f5

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Commits on Dec 7, 2012

• New -t option to vcfcheck and zoomed y-range for ts/tv by sample graph

  pd3

  committed
  ea0da66

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Commits on Nov 29, 2012

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

  pd3

  committed
  0c55d44

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Commits on Nov 28, 2012

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

  pd3

  committed
  97f44b9

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Commits on Nov 23, 2012

• New stats and graphs: singletons and depth by sample; new -s switch; more values in summary table

  pd3

  committed
  ac8e20e

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Commits on Nov 19, 2012

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

  pd3

  committed
  516e1e8

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Commits on Nov 15, 2012

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

  pd3

  committed
  662facb

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• plot-vcfcheck: fixed forgotten .pdf extension string

  pd3

  committed
  86513f8

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• vcfcheck: New stats and graph, allelic r2 by AF; vcf_parse1: error recovery on missing FILTER/INFO/FORMAT tag definitions

  pd3

  committed
  5faf7a2

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Commits on Nov 13, 2012

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

  pd3

  committed
  5be3093

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

  pd3

  committed
  b557ed8

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Commits on Nov 5, 2012

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

  pd3

  committed
  02db06d

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Commits on Oct 17, 2012

• Increase DP stats counter to uint64_t to prevent overflow with big VCFs. On behalf of Chris: plot-vcfcheck can now merge per-chromosome vcfcheck files.

  pd3

  committed
  b2e2287

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Commits on Oct 9, 2012

• Plotting Hets vs Homs instead of plain Hets; Sanity check for FS section header

  pd3

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  3701a81

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Commits on Sep 27, 2012

• Changed order of underscore escaping and line breaking to prevent loss of escape characters

  pd3

  committed
  b92a29b

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Commits on Sep 24, 2012

• New stats: number of RR and AA homs per sample; Version checking

  pd3

  committed
  5290081

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• Fixed forgotten title hash key leading to "No labeled objects" error from matplotlib

  pd3

  committed
  da85f94

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• Prevent failing on near-empty counts_by_AF graphs.

  pd3

  committed
  6359933

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Commits on Sep 4, 2012

• Depth distribution stats

  pd3

  committed
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Commits on Aug 23, 2012

• Always check INFO/AC,AN for by AF stats; TsTv by Qual stats

  pd3

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Commits on Aug 22, 2012

• Fix in calc_ac for missing GTs; Number of MNPs and other events in the summary table

  pd3

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Commits on Aug 21, 2012

• New option --split-by-ID for known vs novel stats

  pd3

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Commits on Aug 10, 2012

• Changed NRD output

  pd3

  committed
  c4b1afd

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Commits on Aug 9, 2012

• Sample list from file or command line; Handle missing GTs in calc_ac and init_iaf; Documented plotting

  pd3

  committed
  1fb0d7e

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Commits on Aug 8, 2012

• Fix in per sample stats; Minor cosmetic improvements of plots

  pd3

  committed
  2ea5600

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• Another vcfcheck stats: NRD by sample

  pd3

  committed
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Commits on Aug 7, 2012

• More vcfcheck stats

  pd3

  committed
  4c27413

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