ebanks ca1917507f Various improvements and fixes: ... In indel cleaner: 1. allow the user to specify that he wants to use Picard’s SAMFileWriter sorting on disk instead of having us sort in memory; this is useful if the input consists of long reads. 2. for N-way-out mode: output bams now use the original headers from the corresponding input bams - as opposed to the merged header. This entailed some reworking of the datasources code. 3. intermediate check-in of code that allows user to input known indels to be used as alternate consenses. Not done yet. In UG: fix bug in beagle output for Jared. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2805 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-07 04:21:04 +00:00
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arguments	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
contexts/variantcontext	Added generic interfaces to RefMetaDataTracker to obtain VariantContext objects. More docs. Integration tests for VariantContexts using dbSNP and VCF. At this stage if you use dbSNP or VCF files only in your walkers, please move them over to the VariantContext, it's just nicer. If you've got RODs that implemented the old variation/genotype interfaces, and you want them to work in new walkers, please add an adaptor to VariantContextAdaptors in refdata package. It should be easy and will reduce burden in the long term when those interfaces are retired.	2010-02-06 16:26:06 +00:00
datasources	Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes	2010-02-05 21:47:54 +00:00
executive	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
io	Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.	2009-09-16 08:33:56 +00:00
iterators	some very old tests relied on cancer data that got moved. Reset one to use data in the validation directory, the other to the artificial sam utils (the best approach).	2010-02-02 23:13:10 +00:00
refdata	Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface.	2010-01-26 13:53:29 +00:00
traversals	First successful test of new sharding system prototype. Can traverse over reads from a single	2010-01-15 03:35:55 +00:00
walkers	Various improvements and fixes:	2010-02-07 04:21:04 +00:00