bam.h

/* The MIT License

   Copyright (c) 2008-2010 Genome Research Ltd (GRL).

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   The above copyright notice and this permission notice shall be
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*/

/* Contact: Heng Li <lh3@sanger.ac.uk> */

#ifndef BAM_BAM_H
#define BAM_BAM_H

/*!
  @header

  BAM library provides I/O and various operations on manipulating files
  in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map)
  format. It now supports importing from or exporting to SAM, sorting,
  merging, generating pileup, and quickly retrieval of reads overlapped
  with a specified region.

  @copyright Genome Research Ltd.
 */


#include <stdint.h>

/*
 * Only small section is pulled out that we use.
 * 4/29/2011 - Mary Kate Trost
 */


/*!
  @abstract    Calculate the minimum bin that contains a region [beg,end).
  @param  beg  start of the region, 0-based
  @param  end  end of the region, 0-based
  @return      bin
 */
static inline int bam_reg2bin(uint32_t beg, uint32_t end)
{
    --end;
    if (beg>>14 == end>>14) return 4681 + (beg>>14);
    if (beg>>17 == end>>17) return  585 + (beg>>17);
    if (beg>>20 == end>>20) return   73 + (beg>>20);
    if (beg>>23 == end>>23) return    9 + (beg>>23);
    if (beg>>26 == end>>26) return    1 + (beg>>26);
    return 0;
}

#endif