Mauricio Carneiro d16cb68539 Updated and more thorough version of the BadCigar read filter ... * No reads with Hard/Soft clips in the middle of the cigar * No reads starting with deletions (with or without preceding clips) * No reads ending in deletions (with or without follow-up clips) * No reads that are fully hard or soft clipped * No reads that have consecutive indels in the cigar (II, DD, ID or DI) Also added systematic test for good cigars and iterative test for bad cigars.		2012-08-17 17:05:27 -04:00
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ReadClipperTestUtils.java	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
ReadClipperUnitTest.java	Fixing unit test	2012-07-06 12:08:09 -04:00