added an option to use varscan readcount methods
remove disk usage from build's web view
improve log format for better parsing
update log reader for new format
ChimerascanResult adds transcripts to bam header

This resolves APIPE-2690
Keep non-primary alignments when filtering

with reuse_bam=1 option we now keep all alignments found in the
Tophat BAM from the rna_seq pipeline.  This resolves APIPE-2691.
Updated blessedness after CNV fixes of RT#89648
Set a memory request.

A recent run took 11.5GB, so set this to 14GB for now.
update clinseq-wer blessed build
allow Rest.psgi to have CPU and memory usage limited

Our web workers fairly frequently persist for many minutes and/or use a
lot of memory so we should be able to limit their CPU and memory usage.
should not assume merged_alignment_bam_path exists
Added a few values that were missing in _resolve_inputs when given a build and not other properties.
Merge branch 'validation' into gb_master
Add queryname sort before the SamToFastq conversion to reduce memory requirement.
added research to valid disk groups
updated jenkins submodule to ff739be
Automatically gather params from sub-annotators
Merge branch 'updated2' into gb_master
Make ChimerascanResult use qname sorted bam
added back in Allison's code to use g m t sam readcount