zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/java/test/org/broadinstitute/sting/playground/gatk/walkers
History
rpoplin 8e31c01680 Solid processing in base quality recalibrator now has several options for how to handle no calls in the color space. --ignore_nocall_colorspace is removed and replace by --solid_nocall_strategy. Fixed some of the @Deprecated tags in BaseUtils. LocusWalkers now filter out FailsVendorQualityCheck reads. HLA caller integration test bam file had bad vendor reads so its integration test changed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3831 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-07-19 19:10:29 +00:00
..
HLAcaller Solid processing in base quality recalibrator now has several options for how to handle no calls in the color space. --ignore_nocall_colorspace is removed and replace by --solid_nocall_strategy. Fixed some of the @Deprecated tags in BaseUtils. LocusWalkers now filter out FailsVendorQualityCheck reads. HLA caller integration test bam file had bad vendor reads so its integration test changed. 2010-07-19 19:10:29 +00:00
annotator The GATK no longer writes vcf3.3; welcome to the world of vcf4.0. Needed to fix a few output bugs to get this to work, but it's looking great. Much more still to come. Guillermo: hopefully this doesn't break your local build too badly. 2010-07-14 04:56:58 +00:00
duplicates forgot to update md5s 2009-12-29 20:31:29 +00:00
poolseq A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests. 2010-04-08 06:14:15 +00:00
validation First step in major cleanup/redo of VCF functionality. Specifically, now: 2010-07-16 22:49:16 +00:00
vcftools First step in major cleanup/redo of VCF functionality. Specifically, now: 2010-07-16 22:49:16 +00:00
ClipReadsWalkersIntegrationTest.java -Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically 2010-03-17 16:00:10 +00:00
HapmapPoolAllelicInfoIntegrationTest.java Hurrr -- this uses power as part of its output. Changes to the power calculation broke the md5s RIGHT AFTER I HAD FIXED THEM arghflrg. 2009-12-14 22:42:50 +00:00