Alec Wysoker c8368ae2a5 Eliminate 7-element arrays in BaseCounts and BaseAndQualsCount and replace with in-line primitive attributes. This is ugly but reduces heap overhead, and changes are localized. When used in conjunction with Mauricio's FastUtil changes it saves and additional 9% or so of execution time.		2013-02-27 12:49:56 -05:00
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gatk	Eliminate 7-element arrays in BaseCounts and BaseAndQualsCount and replace with in-line primitive attributes. This is ugly but reduces heap overhead, and changes are localized. When used in conjunction with Mauricio's FastUtil changes it saves and additional 9% or so of execution time.	2013-02-27 12:49:56 -05:00
utils	Refactored PairHMM.initialize to first take haplotype max length and then the read max length so that it is consistent with other PairHMM methods.	2013-02-25 15:04:23 -05:00
package-info.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00