David Roazen 31827022db Fix pipeline tests that were not respecting the pipeline test dry run setting ... There are a few pipeline test classes that do not run Queue, but are classified as pipeline tests because they submit farm jobs. Make these unconventional pipeline tests respect the pipeline test dry run setting.		2013-06-28 15:27:17 -04:00
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R	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Fix pipeline tests that were not respecting the pipeline test dry run setting	2013-06-28 15:27:17 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Fix pipeline tests that were not respecting the pipeline test dry run setting	2013-06-28 15:27:17 -04:00
testdata	Somehow the index of exampleDBSNP.vcf was missing	2013-05-28 15:29:43 -04:00