Eric Banks ef87b18e09 In retrospect, it wasn't a good idea to have FisherStrand handle reduced reads since they are always on the forward strand. For now, FS ignores reduced reads but I've added a note (and JIRA) to make this work once the RR het compression is enabled (since we will have directionality in reads then).		2012-12-05 02:00:35 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	In retrospect, it wasn't a good idea to have FisherStrand handle reduced reads since they are always on the forward strand. For now, FS ignores reduced reads but I've added a note (and JIRA) to make this work once the RR het compression is enabled (since we will have directionality in reads then).	2012-12-05 02:00:35 -05:00
test	Quick fix: base qual array in the GATKSAMRecord stores the actual phred values (-33) and not the original bytes (duh).	2012-12-03 12:18:20 -05:00