ebanks 3596c56602 New attempt at the constrained movement version of the indel realigner (I've kept around the old writer for now). The new contract is that the realigner must ask permission before trying to clean an area; permission will be denied by the CM-Manager if it was required to flush its cache of reads because of too much depth within a distance of maxInsertSizeForMovingReadPairs. Added integration tests to cover different max cache sizes, including an expected exception when too small a value is chosen. The actual logic changes were fairly minor - much of this commit is really just some cleanup. I'd like to throw 1000G Phase I at it, but will respectfully wait for Ryan to hit his deadline before doing so. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5414 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-10 02:48:29 +00:00
..
OutputStreamArgumentTypeDescriptor.java	Fixed recently introduced multiplexer issue where DoC couldn't be written	2010-12-14 19:35:15 +00:00
OutputStreamStub.java	Play nice with other jobs in this VM -- don't close stdout / stderr.	2009-09-17 18:55:08 +00:00
SAMFileReaderArgumentTypeDescriptor.java	Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong.	2010-09-12 14:02:43 +00:00
SAMFileWriterArgumentTypeDescriptor.java	Fixed recently introduced multiplexer issue where DoC couldn't be written	2010-12-14 19:35:15 +00:00
SAMFileWriterStub.java	New attempt at the constrained movement version of the indel realigner (I've kept around the old writer for now). The new contract is that the realigner must ask permission before trying to clean an area; permission will be denied by the CM-Manager if it was required to flush its cache of reads because of too much depth within a distance of maxInsertSizeForMovingReadPairs. Added integration tests to cover different max cache sizes, including an expected exception when too small a value is chosen. The actual logic changes were fairly minor - much of this commit is really just some cleanup. I'd like to throw 1000G Phase I at it, but will respectfully wait for Ryan to hit his deadline before doing so.	2011-03-10 02:48:29 +00:00
Stub.java	General-purpose management of output streams.	2009-08-23 00:56:02 +00:00
VCFWriterArgumentTypeDescriptor.java	Moving the --sites_only argument up into the VCFWriter itself so that any walkers that write VCFs can choose not to emit genotypes	2011-01-26 19:38:16 +00:00
VCFWriterStub.java	Moving the --sites_only argument up into the VCFWriter itself so that any walkers that write VCFs can choose not to emit genotypes	2011-01-26 19:38:16 +00:00