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gatk-3.8/java/src/org/broadinstitute/sting/gatk
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ebanks 9b2fcc4711 Refactoring of the annotation system: 
1. VA is now a ROD walker so it no longer requires reads (needs a little more testing)
2. Annotations can now represent multiple INFO fields (i.e. sets of key/value pairs)
3. The chromosome count annotations have been pulled out of UG and the VCF writer code and into VA where they belong.  Fixed the headers too.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3513 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-06-09 17:05:51 +00:00
..
arguments Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere. 2010-05-30 18:00:12 +00:00
contexts JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout. 2010-06-07 00:33:02 +00:00
datasources updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function. 2010-06-04 06:34:26 +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 Fail fast if users try to parallelize a read walker. 2010-06-03 18:14:33 +00:00
filters GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line 2010-06-02 22:26:32 +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 Partial flattening of the hanger data structure. Hanger data structure is 2010-06-09 16:28:49 +00:00
refdata Refactoring of the annotation system: 2010-06-09 17:05:51 +00:00
traversals Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end. 2010-05-26 22:12:25 +00:00
walkers Refactoring of the annotation system: 2010-06-09 17:05:51 +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 Experimental versions of downsampler and Ryan's deduper are now available either 2010-05-19 05:40:05 +00:00
DownsamplingMethod.java Experimental versions of downsampler and Ryan's deduper are now available either 2010-05-19 05:40:05 +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 updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function. 2010-06-04 06:34:26 +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