Valentin Ruano-Rubio 7acf2eb0e7 Added a more efficient implementation of the KBest haplotype finder code. ... Story: https://www.pivotaltracker.com/story/show/66238286 Changes: 1. Created a new k-best haplotype search implementation in class KBestHaplotypeFinder. 2. Changed HC code to use the new implementation. This seems to fix the original problem without causing significant changes in outputs using some empirical data test cases 3. Moved haplotype's cigar calculation code from Path to CigarUtils; need that in order to gain independence from Path in some parts of the code. In any case that seems like a more natural location for that functionality.		2014-03-04 12:22:14 -05:00
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src	Added a more efficient implementation of the KBest haplotype finder code.	2014-03-04 12:22:14 -05:00
pom.xml	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00