Mauricio Carneiro 0d976d6211 Fixed second time clipping ... When a read is clipped once, and then in the second operation, because of indels, it doesn't reach the coordinate initially set for hard clipping, the indices were wrong. This should fix it.		2011-08-15 12:04:53 -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	Fixed second time clipping	2011-08-15 12:04:53 -04:00
test	Removed a public -> private dependency in our test suite.	2011-08-12 17:29:10 -04:00