Mauricio Carneiro 17cc484dbd Revert "ReduceReads ref bases are now output as '=' ... 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.		2011-11-01 16:35:07 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Revert "ReduceReads ref bases are now output as '='	2011-11-01 16:35:07 -04:00
test	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00