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gatk-3.8/public/java/test
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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
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net/sf Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not. 2011-07-27 22:06:23 -04:00
org/broadinstitute/sting Added REVERT_SOFTCLIPPED_BASES capability to ReadClipper 2011-12-20 00:04:30 -05:00