Fixed a CRAM support bug for fq2bam.
Fixed a CRAM support bug for human_par.
Two sources of deadlock in lofreq are fixed.
STAR deadlock bug is fixed.
Fix an assertion failure in rna_fq2bam: ReadAlign_outputTranscriptCIGARp.cpp:81:string chimericDetector::outputTranscriptCIGARp_pb(const chimericTrans&, PBWindow*): Assertion P.readFilesIn.size() > 1 failed.
Fix a possibility of a deadlock in rna_fq2bam.
Remove duplicate @HD lines in the output of rna_fq2bam.
Output of collectmultiplemetrics is now correctly tab separated, instead of using spaces.
Use of the --gen-insert-size option would cause the code to fail.
The --gen-all-metrics option failed to create the sequencing artifact report. It now correctly generates all available reports.
Fix a report generation bug for collectmultiplemetrics when --gen-alignment or --gen-insert-size was specified.