libStatGen Software
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bam.h
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/* The MIT License
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Copyright (c) 2008-2010 Genome Research Ltd (GRL).
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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*/
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/* Contact: Heng Li <lh3@sanger.ac.uk> */
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#ifndef BAM_BAM_H
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#define BAM_BAM_H
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/*!
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@header
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BAM library provides I/O and various operations on manipulating files
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in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map)
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format. It now supports importing from or exporting to SAM, sorting,
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merging, generating pileup, and quickly retrieval of reads overlapped
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with a specified region.
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@copyright Genome Research Ltd.
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*/
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#include <stdint.h>
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/*
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* Only small section is pulled out that we use.
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* 4/29/2011 - Mary Kate Trost
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*/
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/*!
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@abstract Calculate the minimum bin that contains a region [beg,end).
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@param beg start of the region, 0-based
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@param end end of the region, 0-based
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@return bin
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*/
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static
inline
int
bam_reg2bin(uint32_t beg, uint32_t end)
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{
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--end;
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if
(beg>>14 == end>>14)
return
4681 + (beg>>14);
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if
(beg>>17 == end>>17)
return
585 + (beg>>17);
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if
(beg>>20 == end>>20)
return
73 + (beg>>20);
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if
(beg>>23 == end>>23)
return
9 + (beg>>23);
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if
(beg>>26 == end>>26)
return
1 + (beg>>26);
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return
0;
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}
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#endif
samtools
bam.h
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