Eric Banks 6996a953a8 Haplotype/Allele based optimizations for the HaplotypeCaller that knock off nearly 20% of the total runtime (multi-sample). ... These 2 changes improve runtime performance almost as much as Ryan's previous attempt (with ID-based comparisons): * Don't unnecessarily overload Allele.getBases() in the Haplotype class. * Haplotype.getBases() was calling clone() on the byte array. * Added a constructor to Allele (and Haplotype) that takes in an Allele as input. * It makes a copy of he given allele without having to go through the validation of the bases (since the Allele has already been validated). * Rev'ed the variant jar accordingly. For the reviewer: all tests passed before rebasing, so this should be good to go as far as correctness.		2013-02-21 10:14:11 -05:00
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helpTemplates	Added several more info types / annotations to GATKDocs	2013-02-21 03:12:40 -05:00
repository	Haplotype/Allele based optimizations for the HaplotypeCaller that knock off nearly 20% of the total runtime (multi-sample).	2013-02-21 10:14:11 -05:00
ivysettings.properties	Moved build.xml, ivy.xml and settings to root of Sting repository.	2009-03-18 19:13:19 +00:00
ivysettings.xml	Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component.	2012-10-16 02:22:30 -04:00