zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/public/java/src/org/broadinstitute/sting/gatk
History
Mauricio Carneiro c210b7cde4 Merge GATK repo into CMI-GATK 
Bringing in the following relevant changes:
	* Fixes the indel realigner N-Way out null pointer exception DEV-10
	* Optimizations to ReduceReads that bring the run time to 1/3rd.

Conflicts:
	protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java

DEV-10 #resolve #time 2m
 		2012-10-23 10:59:11 -04:00
..
arguments MaxAltAlleles now defaults to 6, no more MaxAltAllelesForIndels 2012-10-22 13:47:56 -04:00
contexts Don't try to left align indels in unmapped reads (which for some reason can still have CIGARs) because the ref context is null. 2012-08-29 15:01:11 -04:00
datasources Missing file are user errors. 2012-10-12 09:48:12 -04:00
downsampling PerSampleDownsamplingReadsIterator: fix for incorrect use of DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL 2012-09-21 22:43:39 -04:00
examples Adding categories for the remaining uncategorized walkers 2012-07-30 11:35:08 -04:00
executive Retiring TraverseReads and TraverseLoci after testing confirms nano scheduler version in single threaded version is fine 2012-10-22 16:55:06 -04:00
filters Fix docs for BadMateFilter 2012-10-12 08:35:45 -04:00
io Fixed yet another NPE related to the ArgumentTypeDescriptor vs. ArgumentMatchValue. Added integration test based on GSA-621. 2012-10-22 12:05:32 -04:00
iterators 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
phonehome New GATK argument interface for data and cpu threads 2012-09-05 15:45:24 -04:00
refdata Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers 2012-08-30 10:15:10 -04:00
report Ready for full-scale evaluation adaptive BQSR contexts 2012-08-03 16:02:53 -04:00
resourcemanagement Fixed bug in ThreadAllocation getTotalNumberOfThreads 2012-09-05 16:35:32 -04:00
samples 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
traversals Retiring TraverseReads and TraverseLoci after testing confirms nano scheduler version in single threaded version is fine 2012-10-22 16:55:06 -04:00
walkers Merge GATK repo into CMI-GATK 2012-10-23 10:59:11 -04:00
CommandLineExecutable.java Update URL for phone home / GATK key documentation output by the GATK upon error 2012-08-08 09:29:54 -04:00
CommandLineGATK.java Update the out of space error to include another permutation 2012-10-12 09:38:12 -04:00
GenomeAnalysisEngine.java Re-allow running the GATK with experimental downsampling 2012-09-21 23:20:46 -04:00
ReadMetrics.java Mark I NanoScheduling TraverseLoci 2012-09-05 15:45:23 -04:00
ReadProperties.java Experimental, downsampler-friendly read shard balancer 2012-09-21 22:17:58 -04:00
WalkerManager.java Downsampling: experimental engine integration 2012-09-06 15:03:27 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00