/usr/include/io_lib/binning.h is in libstaden-read-dev 1.13.7-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 | /*
* Copyright (c) 2014 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
*
* 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
* Institute nor the names of its contributors may be used to endorse
* or promote products derived from this software without specific
* prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
* IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
* TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
* PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
* LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
/*
* Author: James Bonfield, Wellcome Trust Sanger Institute. 2014
*/
#ifndef CRAM_BINNING_H
#define CRAM_BINNING_H
/* See http://res.illumina.com/documents/products/whitepapers/whitepaper_datacompression.pdf */
static unsigned int illumina_bin[256] = {
0, /* 0 reserved for N */
1, /* Unused, but for completeness */
6, 6, 6, 6, 6, 6, 6, 6, /* 2-9 */
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, /* 10-19 */
22, 22, 22, 22, 22, /* 20-24 */
27, 27, 27, 27, 27, /* 25-29 */
33, 33, 33, 33, 33, /* 30-34 */
37, 37, 37, 37, 37, /* 35-39 */
40, 40, 40, 40, 40, 40, 40, 40, 40, 40, /* 40+ */
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40,
};
static unsigned int illumina_bin_33[256] = {
0+33,
1+33,
6+33, 6+33, 6+33, 6+33, 6+33, 6+33, 6+33, 6+33,
15+33, 15+33, 15+33, 15+33, 15+33, 15+33, 15+33, 15+33, 15+33, 15+33,
22+33, 22+33, 22+33, 22+33, 22+33,
27+33, 27+33, 27+33, 27+33, 27+33,
33+33, 33+33, 33+33, 33+33, 33+33,
37+33, 37+33, 37+33, 37+33, 37+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
40+33, 40+33, 40+33, 40+33, 40+33, 40+33,
};
enum quality_binning {
BINNING_NONE = 0,
BINNING_ILLUMINA = 1,
};
#endif /* CRAM_BINNING_H */
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