Update cn_mops.py

Proposing these changes as I've seen errors coming from the (experimental) ``calcFractionalCopyNumbers`` function but same analyses finish fine using ``calcIntegerCopyNumbers``.
Merge pull request #565 from kern3020/master

Simplified RNA get data script a bit
Enable detection of sample mixups with 'mixup_check' input parameter. Enable for standard and variant calling pipelines. Ensure correct handling of integer batch names
Improve BED preparation by moving creation of merged BED files to initial steps. Avoids potential race conditions when processing the same file in parallel over multiple chromosomes during initial runs
Fix VarScan header output to be compatible with other callers. Enables usage of VarScan in ensemble calling
Merge pull request #564 from mjafin/patch-4

Update cn_mops.py
Enable passing command line arguments to GATK HaplotypeCaller. Thanks to Severine Catreux
Strip UCSC browser commands from input BED files during preparation. Fixes #566
SNAP aligner: use streaming de-duplication and sorting with samblaster and sambamba
Improve detection of paired ends for large single end files. Better scale GATK HaplotypeCaller joint calling by making use of cores and memory on multi-core runs
Fix memscale usage for GATK joint calling, avoiding breaking previous usages of memscale.
Move qsignature summary output to final project directory. Thanks to @mjafin
Pass full joint called output file to validation instead of individual sample inputs
v0.8.1 release
Merge remote-tracking branch 'upstream/master'
Be more agressive with system memory usage: detect total system memory instead of available and calculate fraction amounts instead of rounding to integer. Goal is to maximize memory usage in complement with previous Java memory fixes
Fix FreeBayes tumor/normal calling for MNPs. Split out MNPs prior to applying vcfsamplediff evaluation and somatic calling, otherwise VT tags do not get passed to split items and all will be filtered. Improve filtering and qualities based on FreeBayes mailing list discussion
Fix for VarDict output in regions with non-N ambiguous bases. Convert them to Ns with awk so GATK is happy
Platypus variant calling fixes: Ensure we only call in regions of interest, remove non-N ambiguous bases, decompose MNPs to allelic primitives
Remove old attempts to manage memory issues by catching re-trying. It never especially helped and new fixes actually resolve the underlying issue