Eric Banks 4fa439d89e Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now		2013-01-09 11:06:10 -05:00
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annotator	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
beagle	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
bqsr	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
compression/reducereads	RR bug fix: we were failing when a read started with an insertion just at the edge of the consensus region.	2012-12-19 10:59:07 -05:00
diagnostics	Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now	2013-01-09 11:06:10 -05:00
diffengine	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
fasta	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
filters	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
genotyper	Move around the DiploidGenotype classes (so it can be used by the GATKPaperGenotyper)	2013-01-08 15:53:11 -05:00
haplotypecaller	Bug fix in the HC's allele mapping for multi-allelic events. Using the allele alone as a key isn't sufficient because alleles change when the reference allele changes during VariantContextUtils.simpleMerge for multi-allelic events.	2013-01-07 11:05:44 -05:00
indels	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
phasing	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
validation	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
varianteval	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
variantrecalibration	Moving integration tests to protected	2013-01-08 09:34:08 -05:00
variantutils	Moving integration tests to protected	2013-01-08 09:34:08 -05:00