Mauricio Carneiro c85100ce9c Fix ClippingOp bug when performing multiple hardclip ops ... bug: When performing multiple hard clip operations in a read that has indels, if the N+1 hardclip requests to clip inside an indel that has been removed by one of the (1..N) previous hardclips, the hard clipper would go out of bounds. fix: dynamically adjust the boundaries according to the new hardclipped read length. (this maintains the current contract that hardclipping will never return a read starting or ending in indels).		2011-12-14 16:57:47 -05:00
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CigarStringTestPair.java	Reorganized the testing code and created ClipReadsTestUtils	2011-12-09 11:52:34 -05:00
ClipReadsTestUtils.java	Fix ClippingOp bug when performing multiple hardclip ops	2011-12-14 16:57:47 -05:00
ClippingOpUnitTest.java	Reorganized the testing code and created ClipReadsTestUtils	2011-12-09 11:52:34 -05:00
ReadClipperUnitTest.java	Fix ClippingOp bug when performing multiple hardclip ops	2011-12-14 16:57:47 -05:00
TestParameter.java	Reorganized the testing code and created ClipReadsTestUtils	2011-12-09 11:52:34 -05:00