tools for early stage alignment file processing

 This package contains some tools for processing BAM files including
 .
   bamsormadup: parallel sorting and duplicate marking
   bamcollate2: reads BAM and writes BAM reordered such that alignment
                 or collated by query name
   bammarkduplicates: reads BAM and writes BAM with duplicate alignments
                 marked using the BAM flags field
   bammaskflags: reads BAM and writes BAM while masking (removing) bits
                 from the flags column
   bamrecompress: reads BAM and writes BAM with a defined compression
                  setting. This tool is capable of multi-threading.
   bamsort: reads BAM and writes BAM resorted by coordinates or
                  query name
   bamtofastq: reads BAM and writes FastQ; output can be collated
                  or uncollated by query name