..
datasources
Use the new downsampling implementation by default
2012-12-10 09:44:50 -05:00
downsampling
Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"
2012-09-10 15:52:39 -04:00
executive
Reorganized the codebase beneath top-level public and private directories,
2011-06-28 06:55:19 -04:00
filters
Updated and more thorough version of the BadCigar read filter
2012-08-17 17:05:27 -04:00
iterators
Use the new downsampling implementation by default
2012-12-10 09:44:50 -05:00
refdata
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
2012-12-19 10:25:22 -05:00
report
Added unit test for outputting sorted GATKReport Tables
2013-01-03 16:53:59 -05:00
samples
Cleanup of VCF header lines and constants, BCF2 bugfixes
2012-06-21 15:16:31 -04:00
traversals
Active Region extensions must stay on contig
2013-01-02 14:46:24 -05:00
walkers
QD is now divided by the average length of the alternate allele (weighted by the allele count). The average length is stored in a related annotation, "AAL", which can be used to re-compute the "old" QD by simple multiplication. Integration tests *should* all pass.
2013-01-02 14:41:29 -05:00
CommandLineGATKUnitTest.java
Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us.
2012-07-18 21:48:58 -04:00
EngineFeaturesIntegrationTest.java
Proper error handling in NanoScheduler
2012-09-19 17:03:13 -04:00
GenomeAnalysisEngineUnitTest.java
Removed the "Walker" suffix from all walkers that had it.
2012-07-20 17:27:11 -04:00
MaxRuntimeIntegrationTest.java
Add GATK-wide command line argument to control the maximum runtime allowed for the GATK
2012-10-26 13:18:34 -04:00
WalkerManagerUnitTest.java
Fixing walker unit test with the new naming convention
2012-07-20 17:50:29 -04:00
c1ba12d71a