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
..
com.google.code.caliper	Killed sonatype repository; it's failed me too many times at this point.	2011-06-09 16:07:02 +00:00
com.google.code.cofoja	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
edu.mit.broad	Rev picard, sam-jdk, and tribble	2013-02-01 13:51:30 -05:00
gov.nist	Adding Jama for Ryan.	2010-04-27 14:30:36 +00:00
net.sf	Rev picard, sam-jdk, and tribble	2013-02-01 13:51:30 -05:00
net.sf.gridscheduler	Switched GridEngine from looking from environment variable to using embedded jar.	2011-07-05 21:59:00 -04:00
net.sf.snpeff	SnpEff 2.0.5 support. Re-enabled SnpEff in the HybridSelectionPipeline.	2012-01-03 15:18:36 -05:00
org.broad	Rev picard, sam-jdk, and tribble	2013-02-01 13:51:30 -05:00
org.broadinstitute	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