bthomas 300a18b85f Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually. ... Note that this functionality will only work if the directory with the fasta is writeable. GATK will fail if directory is read only and and either the .fasta.fai or .dict files don't exist. In the future, we could have these references be created in memory, but we decided against it this time. Locking was also added to ReferenceDataSource so no issues come up while running multiple GATKs on the same reference: we don't want one process to be half-finished and another try to read it. So, you could see error messages related to locking. See ReferenceDataSource.java for explanation of the locking strategy. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3601 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-21 21:42:42 +00:00
..
arguments	First pass at eliminating the old sharding system. Classes required for the original sharding system	2010-06-17 20:17:31 +00:00
contexts	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +00:00
datasources	Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually.	2010-06-21 21:42:42 +00:00
examples	Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes	2010-02-05 21:47:54 +00:00
executive	Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations	2010-06-21 02:11:42 +00:00
filters	Re-allowing blacklist by read group id.	2010-06-16 19:45:44 +00:00
io	Fixed UG parallelization bug. Better integration test to catch this in the future.	2010-05-25 21:03:45 +00:00
iterators	Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations	2010-06-21 02:11:42 +00:00
refdata	GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation.	2010-06-19 21:36:41 +00:00
traversals	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +00:00
walkers	Fix NullPointerException when priority list is left out	2010-06-21 13:46:54 +00:00
CommandLineExecutable.java	Better error message when bam file / list file with wrong extension is	2010-06-03 17:52:48 +00:00
CommandLineGATK.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
DownsampleType.java	We're unable to make the naive deduper more worldly, so we're killing it instead.	2010-06-18 13:54:27 +00:00
DownsamplingMethod.java	We're unable to make the naive deduper more worldly, so we're killing it instead.	2010-06-18 13:54:27 +00:00
GATKErrorReport.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
GenomeAnalysisEngine.java	Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes.	2010-06-18 17:37:11 +00:00
Reads.java	Experimental versions of downsampler and Ryan's deduper are now available either	2010-05-19 05:40:05 +00:00
WalkerManager.java	Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:	2010-05-28 14:52:44 +00:00
package-info.java	Put a major.minor version into the GATK Javadoc for reading. Also,	2010-01-15 21:48:30 +00:00