Mauricio Carneiro 94791a2a75 Add support for reads starting with insertion ... * Modified cleanCigarShift to allow insertions in the beginning and end of the read * Allowed cigars starting/ending in insertions in the systematic ReadClipper tests * Updated all ReadClipper unit tests * ReduceReads does not hard clip leading insertions by default anymore * SlidingWindow adjusts start location if read starts with insertion * SlidingWindow creates an empty element with insertions to the right * Fixed all potential divide by zero with totalCount() (from BaseCounts) * Updated all Integration tests * Added new integration test for multiple interval reducing		2012-01-03 09:29:45 -05:00
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ReadClipperTestUtils.java	Add support for reads starting with insertion	2012-01-03 09:29:45 -05:00
ReadClipperUnitTest.java	Add support for reads starting with insertion	2012-01-03 09:29:45 -05:00