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Commits on Jun 7, 2022

• add batchx badge

  idelvall

  committed
  3e8f9e9

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• add batchx wrapper code

  idelvall

  committed
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Commits on Apr 16, 2019

• Merge branch 'add_pair_read_name'

  ryanlayer

  committed
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• store and print pair read id

  ryanlayer

  committed
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Commits on Apr 11, 2019

• Merge pull request arq5x#300 from brentp/filter-return-0

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  ryanlayer

  authored
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• return 0

  brentp

  committed
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Commits on Feb 13, 2019

• Merge pull request arq5x#290 from brentp/readme

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  ryanlayer

  authored
  800c67c

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• link to smoove

  brentp

  committed
  2ceb55c

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Commits on Jan 8, 2019

• Merge pull request arq5x#284 from brentp/total-reads

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  ryanlayer

  authored
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Commits on Jan 7, 2019

• count total number of aligned reads inside of lumpy_filter

  brentp

  committed
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Commits on Nov 27, 2018

• Merge pull request arq5x#279 from ernfrid/exclude_nonpaired

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  ryanlayer

  authored
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Commits on Nov 26, 2018

• Only include paired-end sequencing reads in discordants file

  ernfrid

  committed
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Commits on Oct 3, 2018

• Merge pull request arq5x#273 from ernfrid/patch-1

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  ryanlayer

  authored
  178d7a6

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• Change make inline functions static inline

  ernfrid

  authored
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Commits on Oct 2, 2018

• Merge pull request arq5x#272 from brentp/extract_sv_reads

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  ryanlayer

  authored
  5b2f4b8

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• match behavior of extract_sv_reads and samblaster

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  brentp

  committed
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Commits on Sep 26, 2018

• Merge pull request arq5x#271 from ernfrid/fix_cram_opts

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  ryanlayer

  authored
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• Changes to get NM in output BAM.

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  ernfrid

  committed
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Commits on Sep 11, 2018

• Merge pull request arq5x#269 from brentp/cram-opts

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  ryanlayer

  authored
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Commits on Sep 10, 2018

• use some cram decode stuff to reduce run-time of lumpy_filter

  brentp

  committed
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Commits on Jun 14, 2018

• Merge pull request arq5x#163 from mvdbeek/py3_lumpy

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  ryanlayer

  authored
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Commits on Jun 6, 2018

• Update README.md

  ryanlayer

  authored
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Commits on Apr 4, 2018

• Merge pull request arq5x#237 from brentp/filter-flags

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  ryanlayer

  authored
  c1bcea1

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• exclude reads that are unmapped, not primary, failing-qc, duplicate

  brentp

  committed
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Commits on Feb 7, 2018

• Merge pull request arq5x#234 from brentp/filter-cram

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  ryanlayer

  authored
  213a417

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• fix travis

  brentp

  committed
  8f74a64

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• support cram in lumpy filter

  brentp

  committed
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Commits on Aug 28, 2017

• Update README.md

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  ryanlayer

  authored
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Commits on Aug 17, 2017

• Update README.md

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  ryanlayer

  authored
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Commits on Apr 21, 2017

• Merge pull request arq5x#187 from brentp/bam_read_error_check

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  ryanlayer

  authored
  649309b

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• Merge pull request arq5x#186 from hall-lab/0.2.13_cram_support

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  ryanlayer

  authored
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Commits on Apr 18, 2017

• filter.c: check return value of sam_read1.

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  brentp

  committed
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Commits on Apr 17, 2017

• Merge branch 'master' into 0.2.13_cram_support

  cc2qe

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Commits on Mar 28, 2017

• allow argument for reference fasta

  cc2qe

  committed
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• Merge branch 'ernfrid-0.2.13_cram_support' into 0.2.13_cram_support

  cc2qe

  committed
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