chartl 88a06ad81f Changes to Depth of Coverage: ... - For speedup in large number of samples, base counts are done on a per read group level, then merged into counts on larger partitions (samples, libraries, etc) + passed all integration tests before next item - Added additional summary item, a coverage threshold. Set by (possibly multiple) -ct flags, the summary outputs will have columns for "%_bases_covered_to_X"; both per sample, and per sample per interval summary files are effected (thus md5s changed for these) NOTE: This is the last revision that will include the per-gene summary files. Once DesignFileGenerator is sufficiently general, and has integration tests, it will be moved to core and the per-gene summary from Depth of Coverage will be retired. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3437 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-26 03:39:22 +00:00
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annotator	a) Made HaplotypeScore default annotation. This changed several integration tests, whose MD5 is now updated.	2010-05-21 22:25:17 +00:00
concordance	Fixing/cleaning up the vcf merge util	2010-03-19 15:13:32 +00:00
coverage	Changes to Depth of Coverage:	2010-05-26 03:39:22 +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 This mean 'Variants' is no longer valid for a ROD type, use GeliText instead.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	Fixed UG parallelization bug. Better integration test to catch this in the future.	2010-05-25 21:03:45 +00:00
indels	Oops, forgot to update integration tests	2010-05-25 20:37:45 +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
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