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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

Commits on Feb 12, 2015

• more changes

  DerrickWood

  committed
  7ca5973

• Add info about --check-names

  DerrickWood

  committed
  d49f3c3

• Make name checking non-default for PE reads

  DerrickWood

  committed
  4b2cbc1

• Cast to silence warning

  DerrickWood

  committed
  04cdc51

Commits on Feb 11, 2015

• Warning cleanup

  DerrickWood

  committed
  d8c879e

• Add rebuild option

  DerrickWood

  committed
  d5cd015

• Display default DB/thread count with usage info

  DerrickWood

  committed
  2d00368

• Reduce memory usage for set_lcas

  DerrickWood

  committed
  93a53d8

• Revert "Switch to sliding window minimum"

  Show description for ef84b13
  DerrickWood

  committed
  ef84b13

Commits on Feb 2, 2015

• Switch to sliding window minimum

  DerrickWood

  committed
  d5daae9

Commits on Jan 28, 2015

• Adding KRAKEN_NUM_THREADS support

  DerrickWood

  committed
  9947443

• Adding per-sequence name translation

  DerrickWood

  committed
  450c599

• Support for new environment variables

  DerrickWood

  committed
  cad40ba

Commits on Jan 21, 2015

• More careful mode change and less redundant making

  DerrickWood

  committed
  fda26c5

• Reduce memory usage for sort

  DerrickWood

  committed
  426921d

• Happy new year

  DerrickWood

  committed
  18f4d22

Commits on Dec 22, 2014

• Shrink using file I/O and counts (not pct)

  DerrickWood

  committed
  864ed3b

Commits on Dec 16, 2014

• support for DB path and default DB

  DerrickWood

  committed
  fc16621

Commits on Dec 14, 2014

• Include full header lines with FASTA/FASTQ output

  DerrickWood

  committed
  86c9cc3

• Improve multi-threaded performance

  DerrickWood

  committed
  7730317

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