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Commits on Sep 10, 2017

• Removed unused arguments

  dfornika

  committed
  cfa43fa

• Added kraken flag --out-fmt

  dfornika

  committed
  79eb24e

Commits on Sep 9, 2017

• Paired/Unpaired output for FASTA/FASTQ

  dfornika

  committed
  57dddcc

• Implemented paired output (with filename prefix)

  dfornika

  committed
  15ad018

Commits on Sep 8, 2017

• Preserve full fastq header (including one whitespace char)

  dfornika

  committed
  0a2c428

• Added fastq output to read merger, using '|' delimiter

  dfornika

  committed
  25505da

• Enable fastq output of classified/unclassified reads in paired mode

  dfornika

  committed
  23ffc82

• Change read separator to '|'

  dfornika

  committed
  6e8c9c2

Commits on Sep 6, 2017

• Merge pull request DerrickWood#82 from dfornika/add-to-library-gb

  Show description for ea138ac
  jenniferlu717

  authored
  ea138ac

Commits on Sep 2, 2017

• Added quote around filename variable to escape metacharacters

  dfornika

  committed
  6c85230

• Simplify decompression, don't check for .gz extension

  dfornika

  committed
  89e6e56

• Support .gbk / .gbff [.gz] files

  dfornika

  committed
  39aaaa0

Commits on Sep 1, 2017

• Replaced /usr/bin/perl with /usr/bin/env perl

  dfornika

  committed
  3c14261

Commits on Aug 28, 2017

• Merge pull request DerrickWood#78 from DerrickWood/revert-76-revert-74-gifix

  Show description for d1b1edd
  DerrickWood

  authored
  d1b1edd

• Fix prelim_map.txt save location

  DerrickWood

  authored
  9a4efe4

• Revert "Revert "Fix to remove dependence on GI numbers""

  jenniferlu717

  authored
  d3fefa8

• Merge pull request DerrickWood#76 from DerrickWood/revert-74-gifix

  Show description for 75327c4
  jenniferlu717

  authored
  75327c4

• Revert "Fix to remove dependence on GI numbers"

  jenniferlu717

  authored
  25cb88c

• Merge pull request DerrickWood#74 from DerrickWood/gifix

  Show description for dad02a0
  jenniferlu717

  authored
  dad02a0

Commits on Aug 27, 2017

• Fix to remove dependence on GI numbers

  DerrickWood

  committed
  79ddbe3

Commits on Mar 3, 2016

• Merge pull request DerrickWood#38 from blankenberg/report-all-unclassified

  Show description for eaf8fb6
  DerrickWood

  committed
  eaf8fb6

• Merge pull request DerrickWood#37 from blankenberg/classify-flush

  Show description for 1e0b9a1
  DerrickWood

  committed
  1e0b9a1

Commits on Feb 25, 2016

• 100 is 100%.

  blankenberg

  committed
  47bb2d3

• Allow kraken-report to work when 0 reads have been classified and --only-classified-output had been specified. Will report 100% of reads as unclassified.

  blankenberg

  committed
  eaa1d79

Commits on Feb 24, 2016

• Flush output files in classify.

  blankenberg

  committed
  cacf33d

Commits on Dec 9, 2015

• Temp fix for bacterial library move on FTP

  DerrickWood

  committed
  5cc8d1a

Commits on May 13, 2015

• installation exit code fix

  DerrickWood

  committed
  adfaa26

Commits on Apr 3, 2015

• Change regex to handle new name format for GRCh38.p2

  DerrickWood

  committed
  feb4397

Commits on Mar 5, 2015

• Version bump

  DerrickWood

  committed
  11a205f

• Clarify error message

  DerrickWood

  committed
  47b7c86

• Fix overflow bug in command line parsing

  DerrickWood

  committed
  6f4ebee

Commits on Feb 18, 2015

• List tweak

  DerrickWood

  committed
  6de8f35

• Documentation - html and markdown updates

  DerrickWood

  committed
  39f7e93

• Plasmids

  DerrickWood

  committed
  6a7e388

Commits on Feb 13, 2015

• Support for pipelined Kraken usage

  DerrickWood

  committed
  7cb3b05

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