Phillip Dexheimer a35f5b8685 Moved arguments controlling options in output files into the engine ... * Arguments involved are --no_cmdline_in_header, --sites_only, and --bcf for VCF files and --bam_compression, --simplifyBAM, --disable_bam_indexing, and --generate_md5 for BAM files * PT 52740563 * Removed ReadUtils.createSAMFileWriterWithCompression(), replaced with ReadUtils.createSAMFileWriter(), which applies all appropriate engine-level arguments * Replaced hard-coded field names in ArgumentDefinitionField (Queue extension generator) with a Reflections-based lookup that will fail noisily during extension generation if there's an error		2014-09-05 21:18:11 -04:00
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src/main/java/org/broadinstitute/gatk/queue/extensions/gatk	Moved arguments controlling options in output files into the engine	2014-09-05 21:18:11 -04:00
pom.xml	Update pom versions to mark the start of GATK 3.3 development	2014-07-17 12:09:33 -04:00