Mauricio Carneiro 8a51732049 Fixes to ReadClipper and added Reference Coordinate clipping. ... * Added reference coordinate based hard clipping functions. This allows you to set a hard cut on where you need the read to be trimmed despite indels. * soft clipping was messing up cigar string if there was already a hard clip at the beginning of the read. Fixed. * hard clipping now works with previously hard clipped reads.		2011-08-14 14:54:33 -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	Fixes to ReadClipper and added Reference Coordinate clipping.	2011-08-14 14:54:33 -04:00
test	Removed a public -> private dependency in our test suite.	2011-08-12 17:29:10 -04:00