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Commits on May 13, 2016

• bug fixes and newer versions of programs

  cboursnell

  committed
  bcc533b

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Commits on Nov 11, 2015

• adding rcorrector

  cboursnell

  committed
  31d67ed

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Commits on Jul 23, 2015

• Merge branch 'master' of github.com:cboursnell/preprocess

  cboursnell

  committed
  08269c4

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Commits on Jul 16, 2015

• fix bowtie2 stats for unpaired reads

  cboursnell

  committed
  097da92

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Commits on Jul 8, 2015

• Merge branch 'master' of github.com:cboursnell/preprocess

  cboursnell

  committed
  da601b2

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• and add combining for single end data

  cboursnell

  committed
  5ece826

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• merged

  cboursnell

  committed
  93beb5b

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• should be easier to rerun

  cboursnell

  committed
  b53b054

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• combine salmon outputs into a single csv file for counts and tpm

  cboursnell

  committed
  0e4159a

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Commits on Jul 7, 2015

• updating cmd class

  cboursnell

  committed
  3cd8948

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• fixes

  cboursnell

  committed
  9b4d4d5

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• Merge branch 'master' of github.com:cboursnell/preprocess

  cboursnell

  committed
  71b7a06

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• bump minor version

  cboursnell

  committed
  140ab14

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• add tests for alignment; fix phred detection for hammer

  cboursnell

  committed
  c7930f5

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• adding salmon alignment from reads

  cboursnell

  committed
  a0eca85

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Commits on Jul 6, 2015

• updating salmon

  cboursnell

  committed
  2b97349

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• added bwa

  cboursnell

  committed
  d43a39c

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Commits on Jun 27, 2015

• Removed reference to facs

  cboursnell

  committed
  0f085ed

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• Added new example and fixed installation instructions

  cboursnell

  committed
  86b8a0d

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Commits on Apr 16, 2015

• update salmon to latest version in deps

  cboursnell

  committed
  2848625

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Commits on Apr 9, 2015

• put test back in for bbnorm

  cboursnell

  committed
  7028cb3

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• remember the location of prenormalised files

  cboursnell

  committed
  ac1c2d6

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• batch operations for bbnorm and hammer

  cboursnell

  committed
  fb933bd

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Commits on Apr 7, 2015

• added running all files through hammer at the same time

  cboursnell

  committed
  fc84556

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• bump version

  cboursnell

  committed
  0233c6b

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• don't run things again if you don't have to

  cboursnell

  committed
  fa97da9

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• make filenames shorter

  cboursnell

  committed
  6bd055b

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Commits on Mar 27, 2015

• more robust java version parsing

  cboursnell

  committed
  de4fe4d

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• fix java version checking

  cboursnell

  committed
  50df4ef

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• update bbnorm to version 34 which outputs 2 files therefore no need for deinterleaving code; bump version

  cboursnell

  committed
  5a2470e

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Commits on Mar 20, 2015

• fix checking for hammer stats

  cboursnell

  committed
  f5279e2

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• don't run hammer stats if already done

  cboursnell

  committed
  47ed22c

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Commits on Mar 19, 2015

• don't run hammer again if output already exists

  cboursnell

  committed
  2383903

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• check threads and memory aren't nil

  cboursnell

  committed
  42d9925

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Commits on Mar 17, 2015

• fix stats generation for trimmomatic

  cboursnell

  committed
  9ab5be0

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