Modification due to cancerscan samples.
Increased threshold for exon skipping & 3p deletion in per-sample view.
New function to copy sample(s) from 'ircr1' to other DB.
New function to merge fastq files.
New function to download fastq files from SGI server.
Changes due to processing new dataset.
New function to add modules to PATH.
New functions to change db table contents automatically.
New global variables for mutect/somaticindeldetector.
Modified routines to process VEP output.
Adds read group information during alignment (bwa/gsnap).
Skipping to call 'AddOrReplaceReadGroup.'
Realignment takes *.dedup.bam as direct input.
Modified to take inputs from cancerscan samples.
To keep the compiler happy.
Compress intermediate .bed file.
New function to draw boxplot for major cancer genes (cancerscan).
Modified to compress trimmed fastq files.
New modules to process indels from somaticindeldetector.
Modified mutect modules to handle both single- and paired- run.
Modified procPileup so that it directly takes input from 'samtools mpileup.'
(no longer produces .pileup file)
Designated volumes for certain types of pipelines.
Modified to take compressed/trimmed fastq files.
xsq2mut,rsq2mut: no need to add read group explicitly.
xsq2mut:skips producing .pileup file, process 'samtools mpileup' output directly.
Added steps to produce CN graph.
Changes due to processing new dataset.
New pipeline to process cancerscan samples.
Merge branch 'master' of https://github.com/SMC1/JK1

Conflicts:
	Integration/cgi/ircr_samp.py