Mauricio Carneiro 9ea40f2e41 Deletions/Insertions in hard clip and bug fixes ... * Deletions now count as hard clipped bases in order to recover the original alignment start of a clipped read. * Insertions do not count as hard clipped bases for the same reason. * This created a bug in the previous cigar cleaning function. Fixed.		2011-09-23 16:37:08 -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	Deletions/Insertions in hard clip and bug fixes	2011-09-23 16:37:08 -04:00
test	Unit test was passing in FORMAT as one of the sample names. There used to be a hack in the VCFHeader to check for this and remove it and I couldn't figure out why, but now I know. Hack was removed and now the unit test passes in only the sample names as per the contract.	2011-09-22 13:28:42 -04:00