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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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David Roazen 1296dd41be Removing the legacy -L "interval1;interval2" syntax 
This syntax predates the ability to have multiple -L arguments, is
inconsistent with the syntax of all other GATK arguments, requires
quoting to avoid interpretation by the shell, and was causing
problems in Queue.

A UserException is now thrown if someone tries to use this syntax.
 		2011-11-21 13:18:53 -05:00
..
CNV Updating md5 because the file changed 2011-09-23 07:33:20 -04:00
annotator Updated header description for the INFO and FORMAT DP fields to be more accurate. 2011-11-17 13:17:53 -05:00
beagle Intermediate (but necessary) fix for Beagle walkers: if a marker is absent in the Beagle output files, but present in the input vcf, there's no reason why it should be omitted in the output vcf. Rather, the vc is written as is from the input vcf 2011-09-13 16:57:37 -04:00
coverage Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
diffengine DiffObjects no longer prints out the file name in the status so MD5 are stable 2011-10-10 15:10:57 -04:00
fasta Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
filters Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two. 2011-08-09 12:04:55 -04:00
genotyper Updated header description for the INFO and FORMAT DP fields to be more accurate. 2011-11-17 13:17:53 -05:00
indels Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative. 2011-10-27 23:55:11 -04:00
phasing Merge branch 'PhaseByTransmission' 2011-11-14 11:31:28 +01:00
qc Removing a public -> private dependency from the test suite. 2011-10-13 21:32:52 -04:00
recalibration Update MD5s for SOLiD recalibration 2011-10-13 18:01:51 -04:00
validation Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative. 2011-10-27 23:55:11 -04:00
varianteval SnpEff 2.0.4 support 2011-11-15 18:36:22 -05:00
variantrecalibration Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts. 2011-09-12 12:17:43 -04:00
variantutils Bug fix in SelectVariants when using a discordance track but no sample specifications. Added integration test to test this. 2011-11-07 15:25:16 -05:00
BAQIntegrationTest.java merge master 2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java Updating MD5s for updated BAM with read groups 2011-10-06 12:15:48 -07:00
PileupWalkerIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PrintReadsIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PrintReadsWalkerUnitTest.java GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00