illumina2bam-tools

#Installation
sudo npm install illumina2bam-tools -g

OR

git clone http://github.com/staliv/illumina2bam-tools.git
cd illumina2bam-tools
sudo npm install . -g

This will create links in the /usr/local/bin/ directory for the existing tools in this package.

##Settings
/usr/local/lib/node_modules/illumina2bam-tools/settings.json

- specify which directory contains the distributed jars from the illumina2bam project
- the scripts will automatically search for the jars by looking recursively one folder "up" from your current working directory (when invoking for example the illumina2bam_demultiplex_wrapper)
- the scripts will try to write to the settings.json file but they will fail (somewhat gracefully) as long as the scripts aren't running as a user with write permissions to the /usr/local/lib/node_modules/illumina2bam-tools/ directory
- specify the directory where your jars are located (in the settings.json file) in order to speed up the process

##Usage

###illumina2bam_demultiplex_wrapper
Wrapper for performing illumina bcl to bam encoding and demultiplexing.

Usage: illumina2bam_demultiplex_wrapper

Options:
-s, --samplesheet Samplesheet [required]
-b, --basecallsDirectory Basecalls directory [required]
-o, --outputDirectory Output directory, sub dirs /project/RunID will be created [required]
-t, --tempDirectory Temp directory, sub dirs will be created [required]
-f Output format [bam|sam], default to 'bam' [default: "bam"]
-v, --verbose Verbose output
-m Maximum mismatches for a barcode to be considered a match [default: 0]
-d Minimum difference between number of mismatches in the best and second best barcodes for a barcode to be considered a match [default: 2]
-n Maximum allowable number of no-calls in a barcode read before it is considered unmatchable [default: 0]
--im Maximum memory heap size for illumina2bam process, defaults to 2g [default: "2g"]
--ib Maximum memory heap size for BamIndexDecoder process, defaults to 1g [default: "1g"]
--debug Parse the first tile in each lane [default: false]
--force Disables check if library already exists, hence overwrites files if the already exist [default: false]
--omitLanes Comma separated list with numbers identifying lanes to omit [default: ""]