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BAM version 2 proposal #259

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Commits on Oct 25, 2017

  1. Tidy up BAM definition

    Split combined fields (bin_mq_nl and flag_nc) into their component
    parts.
    
    Move BIN calculation and Auxiliary tag encoding out of footnotes
    and into their own sections.
    daviesrob committed Oct 25, 2017
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  2. Add BAM version 2

    The magic number is changed to "BAM\2" to allow software to detect
    the new version.
    
    The size of `n_cigar_op` is increased to uint32_t.
    
    An extra field `bam2_hdr_flags` is added to the header, and
    `bam2_flags` is added to the alignment records.  Both of these fields
    are reserved for future enhancements.
    
    The obsolete `bin` field is removed from version 2 files.
    
    A new `BV` tag is added to the SAM `@HD` line as a (rather ugly)
    way of hinting which BAM version should be used.
    daviesrob committed Oct 25, 2017
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Commits on Oct 26, 2017

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