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

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