gatk-3.8

Author	SHA1	Message	Date
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