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/gatk/walkers
History
ebanks ca5b274f16 Unit, integration, and performance tests are all busted, so this is a good time to make a big commit... 
Major cleanup of the genotype writer code from the calling end.  UG no longer supports making calls in anything but VCF, and that allows us to use the VCFWriter more generically now.  Putting the ball in Matt's court to finish collapsing everything.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3996 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-10 04:18:29 +00:00
..
annotator Adding command-line header to VA and VF 2010-08-08 05:21:15 +00:00
coverage Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
fasta Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
filters Adding command-line header to VA and VF 2010-08-08 05:21:15 +00:00
genotyper Unit, integration, and performance tests are all busted, so this is a good time to make a big commit... 2010-08-10 04:18:29 +00:00
indels Re-enabling this test 2010-08-06 20:20:37 +00:00
qc Fixed epic generic paths fail. 2010-05-13 15:59:57 +00:00
recalibration Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
sequenom Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
varianteval Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
variantrecalibration Checking in the tiger team changes. LOD calculation modified. -qScale is back in case people need it. 2010-08-09 20:41:03 +00:00
variantutils Starting the clean up of the sting.utils.genotype code which is all either moving to Tribble, moving to sting.utils.vcf, or being removed. 2010-08-10 02:16:05 +00:00
PileupWalkerIntegrationTest.java Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
PrintReadsWalkerUnitTest.java Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK 2010-05-19 23:27:55 +00:00
VariantsToVCFIntegrationTest.java Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00