Added options to specify input/output filenames (if blank, use sys.stdin/sys.stdout)
Change due to processing new data set
Put all 'makeDB' fuctions into one module.
Added database for CNA using WXS
Added options to specify input/output files (use stdin/stdout by default)
Removed multi-threading option (unstable)
Change due to processing new data set
bam2sortedBed_batch: option to choose which '.bam' to use
Added function to repeat pipelines to all/selected (tumor-normal) pairs
Change due to processing new data set
Changed to use *.recal.bam (duplication removed, realigned, recalibrated) for CNA pipeline
Reduced memory requirement for samtools sort
Add routines & R scripts to make plots of CNA
Added WXS directories.
genePos: return gene's starting positions from refFlat.txt
Reflect change by mygenome module.
Modified to use other modules, adds gene annotations.