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Commits on Jan 7, 2020

• Better length estimation. (PR samtools#1161)

  Show description for 80395dc
  

  whitwham

  authored and

  daviesrob

  committed
  80395dc

Commits on Dec 10, 2019

• Added new tests for optical duplicates.

  Show description for c62a0f1
  

  whitwham

  authored and

  jkbonfield

  committed
  c62a0f1

Commits on Nov 12, 2019

• Updates copyright message for 2019.

  Show description for 72d140b
  

  whitwham

  authored and

  daviesrob

  committed
  72d140b

• Fixed gcc9.2 warning on fprintf.

  Show description for 419f8ac
  

  whitwham

  authored and

  jkbonfield

  committed
  419f8ac

• Added the QC fail condition to optical dupe check. (PR samtools#1134)

  Show description for 264c720
  

  whitwham

  authored and

  daviesrob

  committed
  264c720

Commits on Nov 6, 2019

• Corrected two stat names.

  Show description for fec2446
  

  whitwham

  authored and

  valeriuo

  committed
  fec2446

• More optical duplicate cases covered.

  Show description for 3b92857
  

  whitwham

  authored and

  valeriuo

  committed
  3b92857

Commits on Nov 4, 2019

• Interim commit.

  Show description for 20b8303
  whitwham

  committed
  20b8303

Commits on Oct 30, 2019

• Mostly ref length changes.

  

  whitwham

  authored and

  valeriuo

  committed
  3ccd329

• Changed leftmost variable to hts_pos_t.

  Show description for f6a4f2a
  

  whitwham

  authored and

  valeriuo

  committed
  f6a4f2a

• 64bit upgrade to mpileup.

  

  whitwham

  authored and

  valeriuo

  committed
  97a43b2

• 64 bit upgrades for fixmate, markdup and faidx.

  

  whitwham

  authored and

  valeriuo

  committed
  6c5b9de

Commits on Oct 16, 2019

• Fixes a stats error. (PR samtools#1121)

  Show description for 0ba6505
  

  whitwham

  authored and

  daviesrob

  committed
  0ba6505

Commits on Sep 9, 2019

• Accepts newer name format for optical markdup.

  Show description for 5883427
  whitwham

  committed
  5883427

Commits on Sep 4, 2019

• Changed option name and behaviour.

  Show description for 90dd595
  whitwham

  committed
  90dd595

Commits on Sep 3, 2019

• More review fixes plus additional documentation.

  whitwham

  committed
  82be1ee

Commits on Sep 2, 2019

• Add additional checks after review.

  Show description for 6e7b284
  

  whitwham

  authored and

  daviesrob

  committed
  6e7b284

• Replace magic numbers with #define.

  

  whitwham

  authored and

  daviesrob

  committed
  aa8b4e5

• Small changes after review.

  Show description for f843080
  

  whitwham

  authored and

  daviesrob

  committed
  f843080

• Modified PG writing to fit in with latest code.

  Show description for 9a96b7c
  

  whitwham

  authored and

  daviesrob

  committed
  9a96b7c

• Added help for new options.

  

  whitwham

  authored and

  daviesrob

  committed
  4a62303

• Added a --relaxed mode for duplicate detection.

  Show description for 67cda48
  

  whitwham

  authored and

  daviesrob

  committed
  67cda48

• Initialised variables,

  

  whitwham

  authored and

  daviesrob

  committed
  0557cd1

• Fixed memory error with wrong size stored.

  

  whitwham

  authored and

  daviesrob

  committed
  4a2fb7f

• Added Novaseq coordinate reading code and command line to stats.

  

  whitwham

  authored and

  daviesrob

  committed
  f9415fe

• New -c option to clear old duplicate settings.

  Show description for 9a2e86e
  

  whitwham

  authored and

  daviesrob

  committed
  9a2e86e

• Added temp option to suppress adding @pg line.

  

  whitwham

  authored and

  daviesrob

  committed
  835f8e7

• Added call to add a @pg line using new htslib.

  

  whitwham

  authored and

  daviesrob

  committed
  a306677

• Added an estimated_library_size function.

  Show description for c277744
  

  whitwham

  authored and

  daviesrob

  committed
  c277744

• Simplified optical_duplicate function.

  

  whitwham

  authored and

  daviesrob

  committed
  ad2599f

• Included secondary duplicate marking.

  Show description for 3725da2
  

  whitwham

  authored and

  daviesrob

  committed
  3725da2

• Added 'do' and 'dt' to supplementary and unmapped reads.

  

  whitwham

  authored and

  daviesrob

  committed
  9c727c3

• Added a -d option for optical duplicate distance.

  Show description for 0da0060
  

  whitwham

  authored and

  daviesrob

  committed
  0da0060

• Fix spelling mistake.

  

  whitwham

  authored and

  daviesrob

  committed
  3a29e9a

• Can now write stats to a file with -f.

  

  whitwham

  authored and

  daviesrob

  committed
  262ff2c

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