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gatk-3.8/java/src/org/broadinstitute/sting/gatk
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ebanks 0e9a6826b0 Update to VCF code to get it up to spec. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2917 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-03-03 06:12:42 +00:00
..
arguments Better handling of enums by the command-line argument system. 2010-01-20 21:36:46 +00:00
contexts utility methods for genotype counts 2010-03-02 20:23:41 +00:00
datasources Mediocre implementation of reader pooling within the SAM data source. Will fix this week. 2010-03-02 22:35:02 +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 Stopgap fix for temporary problems sharding when indexless. A more compelling solution will come later this week. 2010-03-02 02:59:14 +00:00
filters Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark. 2010-01-03 21:31:04 +00:00
io Better handling of enums by the command-line argument system. 2010-01-20 21:36:46 +00:00
iterators Clean up the code a bit following the introduction of reduceByInterval. 2010-02-25 01:20:22 +00:00
refdata 1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext. 2010-03-02 20:26:40 +00:00
traversals Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a 2010-02-25 00:16:50 +00:00
walkers Update to VCF code to get it up to spec. 2010-03-03 06:12:42 +00:00
CommandLineExecutable.java Looks bigger than it is: 2010-01-15 00:14:35 +00:00
CommandLineGATK.java Update our error messages to point to getsatisfaction.com/gsa. 2010-01-27 19:16:28 +00:00
GenomeAnalysisEngine.java Locus (non-intervalled) traversal with new sharding system. 2010-03-01 01:58:44 +00:00
Reads.java changes to intelligently log overflowing locus pile-ups. 2010-01-20 08:09:48 +00:00
WalkerManager.java Bug fix for help text / version number - help text retriever was crashing in the debugger if help text hadn't been built. 2010-01-20 19:18:19 +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