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3 Commits (dd990061f6b77ad6db337d5020d8ee4c06e33621)

Author SHA1 Message Date
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