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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
..
VectorPairHMM Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
c After renaming the packages, instead of updating the JNI library used for testing bwa, moving the classes to the archive. 2014-05-19 17:36:41 -04:00
chainFiles The contig is named MT not M in b36. Delivers PT68890442. 2014-04-08 10:03:47 -04:00
doc Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
external-example Various fixes for package tests. 2014-09-04 15:30:31 -04:00
gatk-engine Now passing in the path to the GATK directory to tests. 2014-09-02 01:40:59 +08:00
gatk-queue Now passing in the path to the GATK directory to tests. 2014-09-02 01:40:59 +08:00
gatk-queue-extensions-generator Moved arguments controlling options in output files into the engine 2014-09-05 21:18:11 -04:00
gatk-queue-extensions-public Moved arguments controlling options in output files into the engine 2014-09-05 21:18:11 -04:00
gatk-root Now passing in the path to the GATK directory to tests. 2014-09-02 01:40:59 +08:00
gatk-tools-public Moved arguments controlling options in output files into the engine 2014-09-05 21:18:11 -04:00
gatk-utils Now passing in the path to the GATK directory to tests. 2014-09-02 01:40:59 +08:00
gsalib Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
java/config Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
package-tests Various fixes for package tests. 2014-09-04 15:30:31 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
repo Update GATK to work with latest htsjdk 2014-07-30 12:05:14 -04:00
src/main/scripts/shell For now, executing the delete_maven_links.sh just ahead of creating the symbolic links during the process-test-resources phase. 2014-06-25 02:32:15 +08:00
pom.xml Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00