ebanks 1ec305cd15 Fix for running the cleaner at the lane-level for known indels only: instead of relying on the reads to get the reference sequence, we now use an IndexedFastaSequenceFile in all cases and pad the reference with bases on either end. This allows us to deal with cases in which we are trying to clean just a single deletion-containing read with tiny LOD (so the read needs to be pushed off the seen reference; @Reference doesn't yet work for Read Walkers) and has the added benefit of allowing us now to get much larger known indels that aren't completely covered with reads. ... Thanks to Matt for the advice. Also, for Guillermo: while I was at it, I changed the .stats debug output to emit the original interval instead of the cleaned region. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4058 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-19 11:31:13 +00:00
..
annotator	Alleles are now returned in a consistent order, so we can deal with tri-allelic sites	2010-08-10 15:21:10 +00:00
coverage	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
fasta	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
filters	Adding command-line header to VA and VF	2010-08-08 05:21:15 +00:00
genotyper	Alleles are now returned in a consistent order, so we can deal with tri-allelic sites	2010-08-10 15:21:10 +00:00
indels	Fix for running the cleaner at the lane-level for known indels only: instead of relying on the reads to get the reference sequence, we now use an IndexedFastaSequenceFile in all cases and pad the reference with bases on either end. This allows us to deal with cases in which we are trying to clean just a single deletion-containing read with tiny LOD (so the read needs to be pushed off the seen reference; @Reference doesn't yet work for Read Walkers) and has the added benefit of allowing us now to get much larger known indels that aren't completely covered with reads.	2010-08-19 11:31:13 +00:00
qc	Fixed epic generic paths fail.	2010-05-13 15:59:57 +00:00
recalibration	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
sequenom	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
varianteval	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
variantrecalibration	Memory optimization for the VariantRecalibrator. Only add variants to the list if they pass the novelty and qual filters.	2010-08-17 21:57:28 +00:00
variantutils	Alleles are now returned in a consistent order, so we can deal with tri-allelic sites	2010-08-10 15:21:10 +00:00
PileupWalkerIntegrationTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +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	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00