Mauricio Carneiro f4463d38ca BWA requires pair ended reads to be sorted by read names when operating over BAM files, but Picard sorts by coordinate, so in case we use BWA in pair ended reads, the pipeline now resorts the BAM in read name order, realigns it then sorts it in coordinate order.		2011-06-30 14:29:21 -04:00
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chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Reverting previous change, as promised.	2011-06-30 13:18:30 -04:00
packages	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
scala	BWA requires pair ended reads to be sorted by read names when operating over BAM files, but Picard sorts by coordinate, so in case we use BWA in pair ended reads, the pipeline now resorts the BAM in read name order, realigns it then sorts it in coordinate order.	2011-06-30 14:29:21 -04:00
testdata	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00