rpoplin 3f3f35dea0 UnifiedGenotyper now BAQs via ADD_TAG to facilitate using BAQed quals for GL calculations but unBAQed quals for annotation calculations. UnifiedGenotyper now produces SNP and indel calls simultaneously. 40 base mismatch intrinsic filter removed from UG to greatly simplify the code. RankSumTests are now standard annotations but the integration tests are commented out pending changes that will allow random annotations to work. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5585 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-06 19:06:24 +00:00
..
annotator	UnifiedGenotyper now BAQs via ADD_TAG to facilitate using BAQed quals for GL calculations but unBAQed quals for annotation calculations. UnifiedGenotyper now produces SNP and indel calls simultaneously. 40 base mismatch intrinsic filter removed from UG to greatly simplify the code. RankSumTests are now standard annotations but the integration tests are commented out pending changes that will allow random annotations to work.	2011-04-06 19:06:24 +00:00
beagle	Checked for consistency with the previous integration tests, and updated the walker and test to use the new I/O system (always prints 4 digits on floats.	2011-03-13 15:24:22 +00:00
coverage	-ct x no longer includes coverage in the previous bin	2011-02-24 15:52:04 +00:00
fasta	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Adding integration test for indels in VF	2011-02-11 16:58:57 +00:00
genotyper	UnifiedGenotyper now BAQs via ADD_TAG to facilitate using BAQed quals for GL calculations but unBAQed quals for annotation calculations. UnifiedGenotyper now produces SNP and indel calls simultaneously. 40 base mismatch intrinsic filter removed from UG to greatly simplify the code. RankSumTests are now standard annotations but the integration tests are commented out pending changes that will allow random annotations to work.	2011-04-06 19:06:24 +00:00
indels	Only store a read in the mate hash if it could possibly be moved. This reduces memory consumption especially when dealing with a case of tons of unmapped reads at the end of the bam; however, it's only mildly helpful for chr1 of the Papuans (there's a truly massive pileup 120Mb into it; more thought needed at a later point). Integration tests changed only because some of the reads in the original bam were busted to begin with (it's an old pilot 1000G bam).	2011-04-05 22:20:09 +00:00
phasing	Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.	2010-12-08 17:22:29 +00:00
qc	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
recalibration	Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped.	2010-12-02 18:43:24 +00:00
sequenom	Updated integration test's MD5s reflect the fact that assay sequences were previously designed incorrectly for indels, the bug is now fixed.	2011-01-28 23:00:22 +00:00
varianteval	A better output for Genotype Concordance summary. Now does only % comp hom-ref called hom-ref, het called het, and hom-var called hom-var, which are the quantities we typically show in slides. Updated intergration tests to reflect this change.	2011-03-12 02:03:48 +00:00
variantrecalibration	Minor bug fix in empiricalMu prior calculation in VQSR.	2011-03-10 00:42:38 +00:00
variantutils	Switched the CVUnitTest broken info from an Integer to a String since as of r5383 Integers are no longer broken when converted to Floats.	2011-03-07 16:33:14 +00:00
BAQIntegrationTest.java	Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails.	2011-01-28 15:08:21 +00:00
ClipReadsWalkersIntegrationTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
PileupWalkerIntegrationTest.java	Updated to now longer include 2nd-best base output	2011-04-03 20:13:10 +00:00
PrintReadsIntegrationTest.java	--simplifyBAM is now in the SAMFileWriterArgumentTypeDescriptor, as suggested by map. PrintReads has an integrationtest now that writes out a 1 MB bit of HiSeq normally, with compress 0, and with simplifyBAM on.	2011-03-26 14:57:18 +00:00
PrintReadsWalkerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00