| .. |
|
annotator
|
Reverting back to the old definition of QD because it works better with large numbers of samples. The new QD is relegated to a new annotation: sumGLbyD. Tweaks to the new HaplotypeScore based on evaluation with better QD calculation. The default qual threshold in GenerateVariantClusters is updated to be in line with the variant quality scores coming from the exact model.
|
2011-01-13 14:12:30 +00:00 |
|
beagle
|
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 |
|
coverage
|
Changing testing framework from junit -> testng, for its enhanced configurability.
|
2010-11-01 21:31:44 +00:00 |
|
fasta
|
Changing testing framework from junit -> testng, for its enhanced configurability.
|
2010-11-01 21:31:44 +00:00 |
|
filters
|
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 |
|
genotyper
|
Committing the fragment-based calling code. Results look great in all datasets (will show this at 1000G this week with Ryan). Note that this is an intermediate commit. The code needs to be cleaned up and the fragmentation code needs to be moved up into LocusIteratorByState. This should all happen later this week, but I don't want Ryan to have to keep running from my own personal Sting directory. The current crappy implementation adds ~10% to the runtime, but that should all go away in the next iteration.
|
2011-01-23 05:04:17 +00:00 |
|
indels
|
Changing testing framework from junit -> testng, for its enhanced configurability.
|
2010-11-01 21:31:44 +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
|
Changing testing framework from junit -> testng, for its enhanced configurability.
|
2010-11-01 21:31:44 +00:00 |
|
varianteval
|
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 |
|
variantrecalibration
|
Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.
|
2010-12-14 19:57:20 +00:00 |
|
variantutils
|
<key>=<value> tagging support for command-line arguments. Unfortunately, still
|
2011-01-21 00:22:42 +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 |
|
VariantsToVCFIntegrationTest.java
|
Support for indels in hapmap. This was non-trivial because not only does hapmap not tell you whether the allele is an insertion or deletion, but it also has a completely different positioning strategy (rightmost base). I'll send out an email tomorrow when the new HapMap3.3 VCF is ready.
|
2010-12-27 07:37:46 +00:00 |
2bbcc9275a