rpoplin dffa46b380 BAM files created by TableRecalibration now have the version number and list of covariates used appended to their header with a new 'PG' tag. Eventually the entire list of command line args will be put in there as well. Big thanks to Matt and Aaron. The integration test uses the --no_pg_tag so that the md5 doesn't change every time the version number changes. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2148 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-24 20:53:57 +00:00
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alignment	Basic integration test for the aligner.	2009-11-23 23:08:05 +00:00
gatk	BAM files created by TableRecalibration now have the version number and list of covariates used appended to their header with a new 'PG' tag. Eventually the entire list of command line args will be put in there as well. Big thanks to Matt and Aaron. The integration test uses the --no_pg_tag so that the md5 doesn't change every time the version number changes.	2009-11-24 20:53:57 +00:00
playground/gatk/walkers	The old recalibrator is replaced with the refactored recalibrator. Added a version message to the logger output. These walkers start at version 2.0.0	2009-11-23 14:58:33 +00:00
utils	fix for bug GSA-234: fasta index files couldn't handle anything but letters, numbers, or spaces in the contig name	2009-11-24 19:19:47 +00:00
BaseTest.java	Added some code to change the instrumentation for tests.	2009-05-20 05:15:27 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command.	2009-11-24 02:34:48 +00:00