Mark DePristo ffea6dd95f HaplotypeCaller now has the ability to only consider the best N haplotypes for genotyping ... -- Added a -dontGenotype mode for testing assembly efficiency -- However, it looks like this has a very negative impact on the quality of the results, so the code should be deleted		2013-03-20 22:54:36 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	HaplotypeCaller now has the ability to only consider the best N haplotypes for genotyping	2013-03-20 22:54:36 -04:00
test	AlignmentUtils.calcNumDifferentBases computes the number of bases that differ between a reference and read sequence given a cigar between the two.	2013-03-20 22:54:35 -04:00