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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 9cb3fe3a59 Vastly better way of doing on-demand genotyping loading 
-- With our GenotypesContext class we can naturally create a LazyGenotypesContext subclass that does the on-demand loading.
-- This new class was replaced all of the old, complex functionality
-- Better still, there were many cases were the genotypes were being loaded unnecessarily, resulting in efficiency.  This was detected because some of the integration tests changed as the genotypes were no longer being parsing unnecessarily
-- Misc. bug fixes throughout the system
-- Bug fixes for PhaseByTransmission with new GenotypesContext
 		2011-11-20 08:23:09 -05:00
..
CNV Updating md5 because the file changed 2011-09-23 07:33:20 -04:00
annotator Bug fixes and code cleanup throughout 2011-11-19 18:40:15 -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 Updating MD5s 2011-10-04 15:54:45 -07:00
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 More updates to be consistent with the new rod syntax. 2011-08-09 10:11:37 -04:00
filters Vastly better way of doing on-demand genotyping loading 2011-11-20 08:23:09 -05:00
genotyper Updating MD5 to reflect canonical ordering of calculation 2011-11-19 15:57:33 -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 with master 2011-11-19 09:56:06 -05:00
qc First version of VariantContextBuilder 2011-11-18 11:06:15 -05:00
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