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Commits on Oct 7, 2019

• Prevent index from failing when index already exists

  nikhil

  committed
  df254c5

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Commits on Oct 3, 2019

• Increased version

  nikhil

  committed
  c5c3f7d

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• Fixed cmo_index

  nikhil

  authored
  a6e993b

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Commits on Sep 6, 2019

• Update _version.py

  nikhil

  authored
  f77e811

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Commits on Sep 4, 2019

• Updated indexing tool

  nikhil

  authored
  c232feb

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Commits on Sep 3, 2019

• Added ability to specify fasta path

  nikhil

  authored
  11130ce

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Commits on Jul 5, 2019

• Increased version

  nikhil

  authored
  7d9d98f

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• made split_reads output be gzipped

  timosong

  committed
  81a1d2d

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Commits on Jul 3, 2019

• Merge branch 'master' of https://github.com/mskcc/cmo

  nikhil

  committed
  a8bb40c

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• refactor cmo_split_reads to use linux split command instead

  timosong

  committed
  afb1f51

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Commits on Jul 2, 2019

• Increase chunk size in split_reads; support GRCh37_mm10 in vcf2maf

  ckandoth

  committed
  d82f750

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Commits on Jul 1, 2019

• Increased version

  nikhil

  committed
  6badb9c

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• Changed chunk size

  nikhil

  committed
  df33807

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Commits on Apr 15, 2019

• Increased version number

  nikhil

  committed
  a060c34

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Commits on Apr 12, 2019

• Modified zcat command to work on Mac OS

  nikhil

  committed
  2b1b7e6

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Commits on Mar 18, 2019

• Allow java tmpdir for picard to be configurable

  nikhil

  committed
  b1a04fa

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• Some cleanup

  nikhil

  committed
  7ee2943

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Commits on Mar 15, 2019

• cmo_fillout: Given pairing file, combine TN-counts in same row

  timosong

  committed
  d264c99

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Commits on Dec 7, 2018

• Deduplicate BAMs with the same sample IDs

  ckandoth

  committed
  84c2664

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Commits on Dec 5, 2018

• Fixing java_temp variable setting

  allanbolipata

  authored
  bbe0d36

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Commits on Oct 30, 2018

• cmo_fillout: Skip events with same ref/alt, or blank alt

  ckandoth

  committed
  4bda1b9

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Commits on Oct 11, 2018

• Java heap space for Abra now 18GB x num_samples

  ckandoth

  committed
  fe44107

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Commits on Oct 9, 2018

• Fix for undefined/unused java_temp

  ckandoth

  committed
  e78b488

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Commits on Sep 25, 2018

• Bad regex

  kpjonsson

  committed
  fa51a1b

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Commits on Aug 23, 2018

• Set minimum maq=20/baq=20 to make DMP happy

  ckandoth

  committed
  4cc8c5c

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Commits on Aug 21, 2018

• normalize_vcf will now check-ref to fix REF/ALT issues

  ckandoth

  committed
  3494304

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Commits on Aug 7, 2018

• More runtime heap memory for Abra

  ckandoth

  committed
  bb5b0a0

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• Fix old cmo.utils; update resources.json

  ckandoth

  committed
  5698994

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Commits on Aug 3, 2018

• Allow input of one or more VCFs

  ckandoth

  committed
  820e84a

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Commits on Aug 1, 2018

• Fix bugs in cmo_bcftools

  ckandoth

  committed
  522cf33

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Commits on Jul 10, 2018

• Use files under ramdisk /dev/shm/ifs/depot/pi if found

  ckandoth

  committed
  6f74c71

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Commits on Jul 6, 2018

• Remove fireworks as dependency, deployers must install manually

  ckandoth

  committed
  e5f0b0c

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Commits on Jun 27, 2018

• Tweak some igv_plotter settings

  ckandoth

  committed
  8fa7f64

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• Sample names in DMP BAMs are in RG tag ID not SM

  ckandoth

  committed
  5b37e5b

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Commits on Jun 26, 2018

• Merge branch 'master' of https://github.com/mskcc/cmo

  timosong

  committed
  bcc973f

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