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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examples	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
lib	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
org/broadinstitute/sting/queue/qscripts	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