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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src/org/broadinstitute/sting	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
test/org/broadinstitute/sting	Merge pull request #45 from broadinstitute/mc_fix_indelrealigner_GSA-774	2013-02-19 16:16:48 -08:00