/usr/include/SeqLib/SeqLibCommon.h is in libseqlib-dev 1.1.1+dfsg-5.
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 | #ifndef SEQLIB_COMMON_H
#define SEQLIB_COMMON_H
/*! \mainpage SeqLib 1.0
*
* \section intro_sec Introduction
*
* SeqLib is a C++ package for querying BAM/SAM/CRAM files with HTSlib, performing
* BWA-MEM operations in memory, and peforming sequence assembly with FermiKit.
* See https://github.com/walaj/SeqLib for
* full description.
*/
#include <string>
#include <vector>
/** HTSlib/BWA-MEM/BLAT/Fermi operations */
namespace SeqLib {
static const char RCOMPLEMENT_TABLE[128] = {' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
' ',' ',' ',' ',' ','T',' ','G',' ',' ',' ','C',' ',' ',' ',' ',' ',' ','N',' ',
' ',' ',' ',' ','A',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ','t',' ','g',
' ',' ',' ','c',' ',' ',' ',' ',' ',' ','n',' ',' ',' ',' ',' ','a',' ',' ',' ',
' ',' ',' ',' ',' ',' ',' ',' '};
/*
static const std::vector<std::string> CHR_NAME {"1", "2", "3", "4", "5", "6", "7", "8", "9",
"10", "11", "12", "13", "14", "15", "16", "17",
"18", "19", "20", "21", "22", "X", "Y", "M"};
static const std::vector<std::string> CHR_NAME_NUM {"1", "2", "3", "4", "5", "6", "7", "8", "9",
"10", "11", "12", "13", "14", "15", "16", "17",
"18", "19", "20", "21", "22", "23", "24"};
static const std::vector<int> CHR_LEN_VEC = {249250621, 243199373, 198022430, 191154276, //1-4
180915260, 171115067, //5-6
159138663, 146364022, 141213431, 135534747, 135006516, 133851895, //7-12
115169878, 107349540, 102531392, 90354753, 81195210, 78077248, //13-18
59128983, 63025520, 48129895, 51304566, 155270560, 59373566, //19-24
16571}; //25
static const std::vector<double> CHR_CUMSUM_WEIGHT_X = {0.08209014, 0.16218732, 0.22740558, 0.29036182, 0.34994586, 0.40630223, 0.45871420,
0.50691887, 0.55342720, 0.59806527, 0.64252937, 0.68661320, 0.72454415, 0.75989948,
0.79366797, 0.82342611, 0.85016757, 0.87588214, 0.89535614, 0.91611346, 0.93196494,
0.94886198, 1.00000000};
static const std::vector<double> CHR_WEIGHT_X = {0.08209014, 0.08009718, 0.06521825, 0.06295624, //1-4
0.05958404, 0.05635637, //5-6
0.05241197, 0.04820467, 0.04650833, 0.04463807, 0.04446410, 0.04408383, //7-12
0.03793095, 0.03535534, 0.03376849, 0.02975814, 0.02674146, 0.02571457,
0.01947400, 0.02075732, 0.01585148, 0.01689705, 0.05113802};
static const int CHR_LEN [25] = {249250621, 243199373, 198022430, 191154276, //1-4
180915260, 171115067, //5-6
159138663, 146364022, 141213431, 135534747, 135006516, 133851895, //7-12
115169878, 107349540, 102531392, 90354753, 81195210, 78077248, //13-18
59128983, 63025520, 48129895, 51304566, 155270560, 59373566, //19-24
16571}; //25
static const uint32_t CHR_CLEN [25] = {0, 249250621, 492449994, 690472424, 881626700, 1062541960, 1233657027,
1392795690,1539159712,1680373143,1815907890,1950914406,2084766301,
2199936179, 2307285719, 2409817111, 2500171864, 2581367074, 2659444322,
2718573305, 2781598825, 2829728720, 2881033286, 3036303846, 3095677412};
static const uint32_t genome_size_XY = 3095677411;
static std::string const REFHG19 = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
static const int NONCENT_CHR [44] = {1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,
11,11,12,12,13,14,15,16,16,17,17,18,18,19,19,20,20,21,21,22,23,23,24,24};
*/
}
#endif
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