*Added the functions to turn a BLASR generated BAM file into a usable BAM file.
*Modified the bwa parameters according to test results from NA12878 pb2k dataset.
resolved conflicts by maintaining all the changes in UNSTABLE where this bug had already been fixed.
Conflicts:
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
b) More useful AC,AF logging in VariantsToTable with multiallelic sites: instead of logging comma-separated values, log max value by default. Hidden, experimental argument -logACSum to log sum of ACs instead. This is due to extreme slowness of R in parsing strings to tokens and computing max/sum itself (~100x slower than gatk).
c) Added integrationtest for new SelectVariants commands
Instead of creating a bam list file, I dynamically create a scala list and pass as parameters. This way the intermediate bam files don't get deleted before they should.
It is time to bring the ReadClipper class to the main repo. Read Clipper has tested functionality for soft and hard clipping reads. I will prepare thorough documentation for it as it will be very useful for the assembler and the GATK in general.
b) More R-friendly VariantsToTable printing of AC in case of multiple alt alleles
c) Rename FixPLOrderingWalker to FixGenotypesWalker and rewrote: no longer need older code, replaced with code to replace genotypes with all-zero PL's with a no-call.
The DPP was not using the parameter correctly. It didn't matter for the default option (which is the only one we have been testing) but it would not work for knowns only or smith waterman. It is fixed now.
It now complies with the new rod binding framework.
- Ability to pass a different resident memory reservation and limits. Useful for large pileups of low pass genome data that sometimes need high -Xmx6g but usually don't exceed 2-3g in actual heap size.
- Fixed jobPriority to work for all job runners. Now must be a integer between 0 and 100- even for GridEngine- and will be mapped to the correct values.
- Passing parallel environment and job resource requests to LSF and GridEngine. Useful for passing tokens like iodine_io=1 and -pe pe_slots 8
- Refactored GridEngine JobRunner to also provide basic support for other job dispatchers with DRMAA implementations such as Torque/PBS. Should work for basic running but advanced users must pass their own jobNativeArgs from the command line or in customized QScripts until someone maps properties like jobQueue, jobPriority, residentRequest, etc. into a Torque/PBS/etc. dispatcher.
Eric Banks
Guillermo del Angel
Ryan Poplin
Mauricio Carneiro
Khalid Shakir
Mark DePristo
Roger Zurawicki