..
annotator
Updated GenomicAnnotator integration tests to include the -NO_HEADER argument so that they tests op yelling about trtrivial differences
2011-03-07 23:07:01 +00:00
beagle
There's no reason to special case no-calls if they already have PLs associated with them. Just use the PLs!
2011-01-31 15:05:45 +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
Added several integration tests for UG indel caller:
2011-03-08 16:21:21 +00:00
indels
Adding performance test for case with very high coverage (> 600,000x) over an interval
2011-02-28 19:48:56 +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
Somehow missed this test when I was updating the md5s
2011-03-07 23:53:42 +00:00
variantrecalibration
Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.
2010-12-14 19:57:20 +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
Changing testing framework from junit -> testng, for its enhanced configurability.
2010-11-01 21:31:44 +00:00
PrintReadsWalkerUnitTest.java
Changing testing framework from junit -> testng, for its enhanced configurability.
2010-11-01 21:31:44 +00:00
00ac51acc8