6 Commits (e199562c2521032abd003bd315cbfad294208e93)

Author	SHA1	Message	Date
Mark DePristo	63a9ae817a	Ensure thread-safety of CachingIndexedFastaSequenceFile ... -- Cosmetic cleanup of ReadReferenceView -- TraverseReadsNano provides the reference context, since it's thread-safe -- Cleanup CachingIndexedFastaSequenceFile. Add docs, remove unnecessary setters -- Expand CachingIndexedFastaSequenceFileUnitTest to test explicitly multi-threaded safety.	2012-08-27 12:11:54 -04:00
Mark DePristo	daa26cc64e	Print to logger not to System.out in CachingIndexFastaSequenceFile when profiling cache performance	2012-08-17 11:49:02 -04:00
Mark DePristo	0a3172a9f1	Fix for ref 0 bases for Chris ... -- Disturbingly, fixing this bug doesn't actually cause an test failures. -- Wrote a new QCRefWalker to actually check in detail that the reference bases coming into the RefWalker are all correct when comparing against a clean uncached load of the contig bases directly. -- However, I cannot run this tool due to some kind of weird BAM error -- sending this on to Matt	2012-01-24 10:55:09 -05:00
Mark DePristo	9992c373be	Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.	2011-07-17 20:29:58 -04:00
David Roazen	d647ea4fdc	Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache ... non-static to avoid problems when multiple references are used within the same thread (eg., during integration tests). This should kill the intermittent IndelRealignerIntegrationTest failures.	2011-07-01 16:04:30 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, ... removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00