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Commits on Dec 20, 2011

• Corrected typo in the document

  nirav99

  committed
  2346bbe

• Updating README.txt

  nirav99

  committed
  6c41cd4

• Updating the Illumina pipeline manual.

  nirav99

  committed
  fdd441e

Commits on Dec 19, 2011

• Modified cleaning code to delete qseq files if present in BaseCalls directory.

  Show description for ee07bc9
  nirav99

  committed
  ee07bc9

• Changed location of BWA and modified config_params.yml to use that location.

  Show description for 92bd4ed
  nirav99

  committed
  92bd4ed

Commits on Dec 16, 2011

• Updated comments about a specific HiSeq

  nirav99

  committed
  5bba943

• Updated README

  nirav99

  committed
  870f985

• Adding the Pipeline documentation PDF

  nirav99

  committed
  50864fd

Commits on Dec 14, 2011

• Fixed the bug resulting due to typo in variable name

  nirav99

  committed
  f0e8980

• asshaul.rb : Add a missing class implemented by DRD.

  Show description for 694b3d3
  nirav99

  committed
  694b3d3

Commits on Dec 9, 2011

• Corrected the comments

  nirav99

  committed
  b07ce64

Commits on Dec 5, 2011

• Remove the return statement to execute lims upload command

  nirav99

  committed
  3e4cddc

• A new tool to trim specified regions from the Illumina fastq files.

  nirav99

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  9c03c5d

• Fixed the bug of defaulting to sequence even when reference path was specified

  nirav99

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  57f2d2d

• Bug fix: If number of cycles is not specified in FCDefinition.xml, set read length to zero

  nirav99

  committed
  b16d380

• Allow case in-sensitive search to check for "sequence"

  nirav99

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  98811c3

Commits on Dec 1, 2011

• Specify the scale from 0 to maxValue for base quality.

  nirav99

  committed
  f3dbbdc

• Move all CASAVA generated fastq files in their own directory and enable SNP calling at the end

  nirav99

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  9ed592a

Commits on Nov 30, 2011

• Adding the bash scripts to build various jars

  nirav99

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  2e4c933

• Uncommenting the code to start the analysis

  

  p-illumina

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  80357db

Commits on Nov 25, 2011

• A tool to remove reads with incorrect barcodes from Illumina fastq sequence files

  nirav99

  committed
  c647757

Commits on Nov 21, 2011

• Keep casava generated fastq files in its own directory for now

  nirav99

  committed
  58c2666

• Adding missing files

  nirav99

  committed
  b010bb6

• Start using the Jars to build flowcell plan.

  nirav99

  committed
  536838f

• Correct case of an attribute name

  nirav99

  committed
  5d66dab

Commits on Nov 17, 2011

• README.txt for LIMS communication

  nirav99

  committed
  f178be3

• Ah ! Fixed another mistake in printUsage

  nirav99

  committed
  ca683ab

• Fixed printUsage function to show correct position of command line parameters.

  nirav99

  committed
  932cf5c

Commits on Nov 16, 2011

• Extend AnalysisResultUploader to handle capture result upload and validate NewState of LIMS

  nirav99

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  0e34028

Commits on Nov 15, 2011

• Tool to upload analysis results to LIMS

  nirav99

  committed
  acf65a7

• A tool to query LIMS, obtain the list of barcodes used in the flowcell and the

  Show description for 2285ca8
  nirav99

  committed
  2285ca8

• Added the function to unzip sequence files

  nirav99

  committed
  550cd62

Commits on Nov 11, 2011

• MergeDriver now performs cluster job submission

  nirav99

  committed
  dc6b45d

• Utility to merge BAMs

  nirav99

  committed
  e9cef83

Commits on Nov 10, 2011

• A tool to remove read2 from paired read bams. It resets appropriate flags and

  Show description for 483bcfe
  nirav99

  committed
  483bcfe

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