zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
History
Guillermo del Angel cd058dd10f a) Fixed md5 for legit change in UG output that now also no-calls genotypes w/0,0,0 in PL's in SNP case. 
b) First reimplementation of new vc merger of different types. Previous version did it in two steps, first merging all vc's per type and then trying to see if resulting vc's would be merged if alleles of one type were a subset of another, but this won't work when uniquifying genotypes since sample names would be messed up and GT sample names wouldn't match VC sample names. Now, it's actually simpler: when splitting vc's by type before merging, we check for alleles of one vc being a subset of alleles of vc of another type and if so we put them together in same list.
 		2011-09-24 13:40:11 -04:00
..
CNV Updating md5 because the file changed 2011-09-23 07:33:20 -04:00
annotator SnpEff annotator now assigns a functional class to each effect and distinguishes between actual effects and mere modifiers. 2011-09-23 16:06:52 -04:00
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 Moving more tools over to the new rod system 2011-08-10 13:42:35 -04:00
diffengine Spelling fix requires md5 updates 2011-08-26 07:40:44 -04:00
fasta More updates to be consistent with the new rod syntax. 2011-08-09 10:11:37 -04:00
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 a) Fixed md5 for legit change in UG output that now also no-calls genotypes w/0,0,0 in PL's in SNP case. 2011-09-24 13:40:11 -04:00
indels Moving more tools over to the new rod system 2011-08-10 13:42:35 -04:00
phasing Update to new RodBinding system 2011-08-11 17:54:16 -04:00
qc 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
recalibration Fixing syntax of BQSR and UG performance tests. 2011-08-11 17:04:09 -04:00
validation Continuing progress towards RodBinding 1.0 2011-08-03 17:19:28 -04:00
varianteval SnpEff annotator now assigns a functional class to each effect and distinguishes between actual effects and mere modifiers. 2011-09-23 16:06:52 -04:00
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 Merge from stable into unstable 2011-09-22 11:19:43 -04:00
BAQIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ClipReadsWalkersIntegrationTest.java Swapped argument order but not MD5 order 2011-08-19 16:55:56 -04:00
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 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00