depristo 5abac5c057 A few more char -> byte cleanups ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3398 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-20 00:02:06 +00:00
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annotator	Heads up everyone:	2010-04-09 05:37:25 +00:00
concordance	Fixing/cleaning up the vcf merge util	2010-03-19 15:13:32 +00:00
coverage	Got rid of stray unicode characters in copyright message.	2010-05-13 14:47:39 +00:00
fasta	Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase.	2010-04-29 22:50:17 +00:00
filters	Moving VariantFiltration over to use VariantContext.	2010-03-19 18:35:23 +00:00
genotyper	A few more char -> byte cleanups	2010-05-20 00:02:06 +00:00
indels	Added PG tag to bam header to let people know it's been cleaned.	2010-04-30 17:30:30 +00:00
qc	Fixed epic generic paths fail.	2010-05-13 15:59:57 +00:00
recalibration	Fixing the performance tests: we need to catch the RuntimeException (not samtools' RuntimeIOExcpetion). Also, CountCovariates doesn't need the catch.	2010-04-19 14:28:12 +00:00
sequenom	Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it.	2010-04-19 05:47:17 +00:00
varianteval	VE integration test	2010-05-07 13:58:25 +00:00
DepthOfCoverageIntegrationTest.java	Major refactoring of Depth of Coverage to allow for more extensible partitions of data (now can do read group, sample, and library; in any combination; adding more is fairly easy). Changed the by-gene code to use clones of stats objects, rather than munging the interval DoCs. (Fix for Avinash. Who, hilariously, thinks my name is Carl.) Added sorting methods to ensure static ordering of header and body fields.	2010-05-18 16:58:13 +00:00
PileupWalkerIntegrationTest.java	Now that we changed how deletions are represented, got to update MD5...	2009-12-30 22:00:58 +00:00
PrintReadsWalkerUnitTest.java	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00
VariantsToVCFIntegrationTest.java	Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase.	2010-04-29 22:50:17 +00:00