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Rm dupes#235

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averagehat wants to merge 38 commits intodevVDBWRAIR/ngs_mapper:devfrom rm-dupesVDBWRAIR/ngs_mapper:rm-dupesCopy head branch name to clipboard

+255-160

Commits

Commits on Mar 23, 2016

• ngs_filter now uses generators

  

  Panciera

  committed
  d0b94bf

• remove tuple argument

  

  Panciera

  committed
  92dc4c7

• fix missing variable definition

  

  Panciera

  committed
  a1797d5

Commits on Mar 24, 2016

• deleting some comments

  averagehat

  committed
  36cc00d

Commits on Mar 25, 2016

• moved from reduce to cytoolz.accumulate

  

  Panciera

  committed
  bda87ee

• explicit generator instead of accumulate

  

  Panciera

  committed
  cd828bf

• Merge branch 'faster-filter' of https://github.com/VDBWRAIR/ngs_mapper into faster-filter

  

  Panciera

  committed
  8362668

Commits on Mar 28, 2016

• print statements -> logger

  

  Panciera

  committed
  719e7a0

• filter now symlinks if qual=0 and dropNs=False

  

  Panciera

  committed
  951bac3

• filter minquality is now 0 to avoid wasted runtime

  

  Panciera

  committed
  3197f2f

• nfilter now uses threads argument/config for parallelism

  

  Panciera

  committed
  1397dc3

• fixed arg schema

  

  Panciera

  committed
  ff63261

• fixed missing =

  averagehat

  committed
  0f85f47

• fix 'w'/'a' bug in stats file, where it got overwritten each read

  

  Panciera

  committed
  3510db4

Commits on Mar 29, 2016

• Closes #221

  necrolyte2

  committed
  999dc98

• attempting to simplify threads for multiprocessing pool

  necrolyte2

  committed
  bf18479

• fixed incorrect function name in pool.map

  necrolyte2

  committed
  3c2f363

• fixing map call even good-er

  necrolyte2

  committed
  1efc9cd

• Merge pull request #226 from VDBWRAIR/fix-221

  Show description for 03ece3f
  averagehat

  committed
  03ece3f

• Merge pull request #228 from VDBWRAIR/faster-filter-pool

  Show description for b3639f1
  averagehat

  committed
  b3639f1

• Merge remote-tracking branch 'origin/master' into faster-filter

  

  Panciera

  committed
  3ed7521

• fixed symlink by using abspath

  

  Panciera

  committed
  da98cc7

Commits on Mar 30, 2016

• Closes #229. Moved qsub argument parsing into parse_args so they can parse the rest of unparsed args if they exist and --qsub_ exist so error can be raised if wrong args exist

  necrolyte2

  committed
  c4702bd

• fixes drop-ns. Closes #229

  necrolyte2

  committed
  c9feddf

• unit tests folder...didn't see them before

  necrolyte2

  committed
  b99c16b

• Merge pull request #215 from VDBWRAIR/faster-filter

  Show description for 3677d30
  necrolyte2

  committed
  3677d30

• Merge pull request #230 from VDBWRAIR/fix-229

  Show description for df39b43
  averagehat

  committed
  df39b43

• include docs link and build steps

  averagehat

  committed
  61cc534

• add documentation link to readme

  averagehat

  committed
  eaacb53

Commits on Apr 6, 2016

• convert_formats now spits out to a new directory

  averagehat

  committed
  3a25c80

• outdir won't exist yet

  averagehat

  committed
  25e46b4

• fix trivial errors

  averagehat

  committed
  f962646

• now symlinks fastq files

  averagehat

  committed
  a1deff9

• no longer remove convert dir (ngs_filter symlinks)

  averagehat

  committed
  a43120e

• filter application never gets called if no filter options

  averagehat

  committed
  187c38c

• fastq reads get gnuzipped after they're used

  averagehat

  committed
  22366ed

• accidentally quoted variable

  averagehat

  committed
  3638195

• Merge branch 'convert-fix' of https://github.com/VDBWRAIR/ngs_mapper into dup-fix

  averagehat

  committed
  9a386a8