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Commits on Feb 12, 2020

• Fix documentation and help string for addreplacerg.

  valeriuo

  committed
  4fc76fe

Commits on Feb 5, 2020

• Use the new method fai_path to retrieve the name of a FAI file.

  Show description for 451834d
  

  valeriuo

  authored and

  daviesrob

  committed
  451834d

Commits on Jan 23, 2020

• Fix target_count size and value. (PR samtools#1174)

  Show description for 383a31b
  

  valeriuo

  authored and

  daviesrob

  committed
  383a31b

Commits on Jan 15, 2020

• Add option (-J) to include deletions in depth computation. (PR samtools#1163)

  

  valeriuo

  authored and

  daviesrob

  committed
  b034693

Commits on Jan 7, 2020

• Add unit test for merging with a BED file.

  

  valeriuo

  authored and

  daviesrob

  committed
  519e90d

• Add BED file interface for merge.

  

  valeriuo

  authored and

  daviesrob

  committed
  5b27a0c

Commits on Dec 6, 2019

• Fix header file for strcasecmp.

  valeriuo

  committed
  6fe0285

Commits on Nov 18, 2019

• Add PG line with split -u.

  valeriuo

  committed
  ef8e24f

Commits on Nov 8, 2019

• [depth] Options for filtering reads (PR samtools#953)

  Show description for 3b0753f
  

  valeriuo

  authored and

  daviesrob

  committed
  3b0753f

Commits on Oct 31, 2019

• In anticipation of samtools/htslib#963

  valeriuo

  committed
  255b776

Commits on Oct 30, 2019

• Add support for long references to coverage command.

  valeriuo

  committed
  42d68ac

• Switch targetcut to long references.

  valeriuo

  committed
  cf444d8

• Add stats tests with 64 bit positions.

  valeriuo

  committed
  f38fa56

• Make stats work with 64 bit positions

  valeriuo

  committed
  f70ca4d

Commits on Oct 1, 2019

• Make -a and -aa behave the same for single region filters. (PR samtools#1113)

  Show description for 796cf22
  

  valeriuo

  authored and

  daviesrob

  committed
  796cf22

Commits on Sep 11, 2019

• Fix RG line tests. (PR samtools#1104)

  

  valeriuo

  authored and

  daviesrob

  committed
  b1e2c78

Commits on Sep 3, 2019

• Add @PG lines with view.

  

  valeriuo

  authored and

  daviesrob

  committed
  1b03b34

Commits on Aug 20, 2019

• Add a PG line when producing a new file.

  Show description for 7eb338f
  

  valeriuo

  authored and

  daviesrob

  committed
  7eb338f

Commits on Aug 19, 2019

• Remove the direct use of header stuct fields.

  Show description for 0cff5ab
  

  valeriuo

  authored and

  daviesrob

  committed
  0cff5ab

• Remove the use of header.l_text (part 2).

  

  valeriuo

  authored and

  daviesrob

  committed
  413d178

• Remove the use of header.l_text (part 1).

  

  valeriuo

  authored and

  daviesrob

  committed
  c3bc790

• Remove the old RG lines with addreplacerg. Use sam_hdr_remove_except.

  

  valeriuo

  authored and

  daviesrob

  committed
  53362c8

• Switch to the new header API methods for reference name and length.

  

  valeriuo

  authored and

  daviesrob

  committed
  4e76835

• Change bam_hdr* to sam_hdr*, with the exception of bam_hdr_read and bam_hdr_write.

  

  valeriuo

  authored and

  daviesrob

  committed
  8a52b07

• Switch to new header API.

  

  valeriuo

  authored and

  daviesrob

  committed
  b44ffdf

Commits on Aug 8, 2019

• Code styling.

  valeriuo

  committed
  76e7ed6

Commits on Jul 31, 2019

• Various fixes.

  valeriuo

  committed
  5970325

Commits on Jul 12, 2019

• Add option --output-sep to set the separator character for tag lists.

  Show description for 3247bfc
  valeriuo

  committed
  3247bfc

• Add option --output-extra to extend the output of mpileup with user selected read fields and tag values.

  valeriuo

  committed
  17a0f8d

Commits on Jul 8, 2019

• Add option --reverse-del to mark deletions on reverse strands with #.

  valeriuo

  committed
  281247c

Commits on Jul 3, 2019

• Minor fixes and rebase.

  valeriuo

  committed
  60effec

Commits on Apr 30, 2019

• Fix proper float division.

  valeriuo

  committed
  87e4ef3

Commits on Apr 4, 2019

• Minor refactoring.

  valeriuo

  committed
  1b72f1a

Commits on Mar 25, 2019

• Refactor the stats code to use the new multi-region iterator interface.

  

  valeriuo

  authored and

  daviesrob

  committed
  8f7b2cd

• Improve the help message of fasta/fastq command.

  

  valeriuo

  authored and

  daviesrob

  committed
  a58e8dc

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