Eric Banks 994a4ff387 Track all outputs from BQSR (.table, .csv., and .pdf) as @Output arguments. Updated integration tests because we no longer have command-line options not to generate plots (now just don't provide a pdf) or to keep the intermediate csv (now, just provide a filename on the command-line). This is currently busted because we can't access the original filenames from the Engine's storage/stub system and therefore cannot call out to the Rscript with the executor (which requires filename strings).		2012-09-12 11:24:53 -04:00
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src/org/broadinstitute/sting	Fix GSA-535: storing likelihoods in allele map was busted when running HaplotypeCaller, only the last likelihood of a haplotype was being stored, as opposed to the max likelihood of all haplotypes mapping to an allele	2012-09-11 11:01:26 -04:00
test/org/broadinstitute/sting/gatk/walkers	Track all outputs from BQSR (.table, .csv., and .pdf) as @Output arguments. Updated integration tests because we no longer have command-line options not to generate plots (now just don't provide a pdf) or to keep the intermediate csv (now, just provide a filename on the command-line). This is currently busted because we can't access the original filenames from the Engine's storage/stub system and therefore cannot call out to the Rscript with the executor (which requires filename strings).	2012-09-12 11:24:53 -04:00