libStatGen Software  1
bam.h
1 /* The MIT License
2 
3  Copyright (c) 2008-2010 Genome Research Ltd (GRL).
4 
5  Permission is hereby granted, free of charge, to any person obtaining
6  a copy of this software and associated documentation files (the
7  "Software"), to deal in the Software without restriction, including
8  without limitation the rights to use, copy, modify, merge, publish,
9  distribute, sublicense, and/or sell copies of the Software, and to
10  permit persons to whom the Software is furnished to do so, subject to
11  the following conditions:
12 
13  The above copyright notice and this permission notice shall be
14  included in all copies or substantial portions of the Software.
15 
16  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
17  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
18  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19  NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
20  BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
21  ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
22  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
23  SOFTWARE.
24 */
25 
26 /* Contact: Heng Li <lh3@sanger.ac.uk> */
27 
28 #ifndef BAM_BAM_H
29 #define BAM_BAM_H
30 
31 /*!
32  @header
33 
34  BAM library provides I/O and various operations on manipulating files
35  in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map)
36  format. It now supports importing from or exporting to SAM, sorting,
37  merging, generating pileup, and quickly retrieval of reads overlapped
38  with a specified region.
39 
40  @copyright Genome Research Ltd.
41  */
42 
43 
44 #include <stdint.h>
45 
46 /*
47  * Only small section is pulled out that we use.
48  * 4/29/2011 - Mary Kate Trost
49  */
50 
51 
52 /*!
53  @abstract Calculate the minimum bin that contains a region [beg,end).
54  @param beg start of the region, 0-based
55  @param end end of the region, 0-based
56  @return bin
57  */
58 static inline int bam_reg2bin(uint32_t beg, uint32_t end)
59 {
60  --end;
61  if (beg>>14 == end>>14) return 4681 + (beg>>14);
62  if (beg>>17 == end>>17) return 585 + (beg>>17);
63  if (beg>>20 == end>>20) return 73 + (beg>>20);
64  if (beg>>23 == end>>23) return 9 + (beg>>23);
65  if (beg>>26 == end>>26) return 1 + (beg>>26);
66  return 0;
67 }
68 
69 #endif