ReduceReads ref bases are now output as '=' to save space

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Restructured the sliding window framework to manipulate a wrapped version of the SAMRecord that contains information about the reference.

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Mauricio Carneiro 2011-10-30 11:57:52 -04:00

parent dbd8c25787

commit 389380a590

1 changed files with 756 additions and 745 deletions

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public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java

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