Revert "ReduceReads ref bases are now output as '='

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Reducing the reference bases to '=' results in an extra compression of 13% on average. The GATK is not ready to handle files with '=' bases, and the decision was to implement this a an engine support, not a part of ReduceReads.

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Mauricio Carneiro 2011-11-01 16:35:07 -04:00

parent 76c32f5409

commit 17cc484dbd

1 changed files with 745 additions and 756 deletions

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

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