5 Commits (ff26f2bf688048bbd6e2b9ffcf31cedce4fa99dd)

Author	SHA1	Message	Date
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
Mauricio Carneiro	17bfe48d5e	Made all class methods private in the ReadClipper ... * ReadClipperUnitTest now uses static methods * Haplotype caller now uses static methods * Exon Junction Genotyper now uses static methods	2011-12-27 02:11:32 -05:00
Mauricio Carneiro	cadff40247	getRefCoordSoftUnclippedStart and End refactor ... These functions are methods of the read, and supplement getAlignmentStart() and getUnclippedStart() by calculating the unclipped start counting only soft clips. * Removed from ReadUtils * Added to GATKSAMRecord * Changed name to getSoftStart() and getSoftEnd * Updated third party code accordingly.	2011-12-20 17:48:51 -05:00
Mauricio Carneiro	78d9bf7196	Added REVERT_SOFTCLIPPED_BASES capability to ReadClipper ... * New ClippingOp REVERT_SOFTCLIPPED_BASES turns soft clipped bases into matches. * Added functionality to clipping op to revert all soft clip bases in a read into matches * Added revertSoftClipBases function to the ReadClipper for public use * Wrote systematic unit tests	2011-12-20 00:04:30 -05:00
Mauricio Carneiro	5b678e3b94	Remove ClippingOp UnitTests ... * all testing functionality is in the ReadClipperUnitTest, no need to double test. * class and package naming cleanup	2011-12-19 07:49:26 -05:00