File: qual.h

package info (click to toggle)
bowtie2 2.4.2-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 27,104 kB
  • sloc: cpp: 60,331; perl: 7,540; sh: 1,111; python: 949; makefile: 520; ansic: 122
file content (235 lines) | stat: -rw-r--r-- 6,589 bytes parent folder | download | duplicates (12)
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
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
/*
 * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
 *
 * This file is part of Bowtie 2.
 *
 * Bowtie 2 is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * Bowtie 2 is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with Bowtie 2.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef QUAL_H_
#define QUAL_H_

#include <stdexcept>
#include "search_globals.h"
#include "sstring.h"

extern unsigned char qualRounds[];
extern unsigned char solToPhred[];

/// Translate a Phred-encoded ASCII character into a Phred quality
static inline uint8_t phredcToPhredq(char c) {
	return ((uint8_t)c >= 33 ? ((uint8_t)c - 33) : 0);
}

/**
 * Convert a Solexa-scaled quality value into a Phred-scale quality
 * value.
 *
 * p = probability that base is miscalled
 * Qphred = -10 * log10 (p)
 * Qsolexa = -10 * log10 (p / (1 - p))
 * See: http://en.wikipedia.org/wiki/FASTQ_format
 *
 */
static inline uint8_t solexaToPhred(int sol) {
	assert_lt(sol, 256);
	if(sol < -10) return 0;
	return solToPhred[sol+10];
}

class SimplePhredPenalty {
public:
	static uint8_t mmPenalty (uint8_t qual) {
		return qual;
	}
	static uint8_t delPenalty(uint8_t qual) {
		return qual;
	}
	static uint8_t insPenalty(uint8_t qual_left, uint8_t qual_right) {
		return std::max(qual_left, qual_right);
	}
};

class MaqPhredPenalty {
public:
	static uint8_t mmPenalty (uint8_t qual) {
		return qualRounds[qual];
	}
	static uint8_t delPenalty(uint8_t qual) {
		return qualRounds[qual];
	}
	static uint8_t insPenalty(uint8_t qual_left, uint8_t qual_right) {
		return qualRounds[std::max(qual_left, qual_right)];
	}
};

static inline uint8_t mmPenalty(bool maq, uint8_t qual) {
	if(maq) {
		return MaqPhredPenalty::mmPenalty(qual);
	} else {
		return SimplePhredPenalty::mmPenalty(qual);
	}
}

static inline uint8_t delPenalty(bool maq, uint8_t qual) {
	if(maq) {
		return MaqPhredPenalty::delPenalty(qual);
	} else {
		return SimplePhredPenalty::delPenalty(qual);
	}
}

static inline uint8_t insPenalty(bool maq, uint8_t qual_left, uint8_t qual_right) {
	if(maq) {
		return MaqPhredPenalty::insPenalty(qual_left, qual_right);
	} else {
		return SimplePhredPenalty::insPenalty(qual_left, qual_right);
	}
}

/**
 * Take an ASCII-encoded quality value and convert it to a Phred33
 * ASCII char.
 */
inline static char charToPhred33(char c, bool solQuals, bool phred64Quals) {
	using namespace std;
	if(c == ' ') {
		std::cerr << "Saw a space but expected an ASCII-encoded quality value." << endl
		          << "Are quality values formatted as integers?  If so, try --integer-quals." << endl;
		throw 1;
	}
	if (solQuals) {
		// Convert solexa-scaled chars to phred
		// http://maq.sourceforge.net/fastq.shtml
		char cc = solexaToPhred((int)c - 64) + 33;
		if (cc < 33) {
			std::cerr << "Saw ASCII character "
			          << ((int)c)
			          << " but expected 64-based Solexa qual (converts to " << (int)cc << ")." << endl
			          << "Try not specifying --solexa-quals." << endl;
			throw 1;
		}
		c = cc;
	}
	else if(phred64Quals) {
		if (c < 64) {
			cerr << "Saw ASCII character "
			     << ((int)c)
			     << " but expected 64-based Phred qual." << endl
			     << "Try not specifying --solexa1.3-quals/--phred64-quals." << endl;
			throw 1;
		}
		// Convert to 33-based phred
		c -= (64-33);
	}
	else {
		// Keep the phred quality
		if (c < 33) {
			cerr << "Saw ASCII character "
			     << ((int)c)
			     << " but expected 33-based Phred qual." << endl;
			throw 1;
		}
	}
	return c;
}

/**
 * Take an integer quality value and convert it to a Phred33 ASCII
 * char.
 */
inline static char intToPhred33(int iQ, bool solQuals) {
	using namespace std;
	int pQ;
	if (solQuals) {
		// Convert from solexa quality to phred
		// quality and translate to ASCII
		// http://maq.sourceforge.net/qual.shtml
		pQ = solexaToPhred((int)iQ) + 33;
	} else {
		// Keep the phred quality and translate
		// to ASCII
		pQ = (iQ <= 93 ? iQ : 93) + 33;
	}
	if (pQ < 33) {
		cerr << "Saw negative Phred quality " << ((int)pQ-33) << "." << endl;
		throw 1;
	}
	assert_geq(pQ, 0);
	return (int)pQ;
}

inline static uint8_t roundPenalty(uint8_t p) {
	if(gNoMaqRound) return p;
	return qualRounds[p];
}

/**
 * Fill the q[] array with the penalties that are determined by
 * subtracting the quality values of the alternate basecalls from
 * the quality of the primary basecall.
 */
inline static uint8_t penaltiesAt(size_t off, uint8_t *q,
                                  int alts,
                                  const BTString&    qual,
                                  const BTDnaString *altQry,
                                  const BTString    *altQual)
{
	uint8_t primQ = qual[off]; // qual of primary call
	uint8_t bestPenalty = roundPenalty(phredcToPhredq(primQ));
	// By default, any mismatch incurs a penalty equal to the quality
	// of the called base
	q[0] = q[1] = q[2] = q[3] = bestPenalty;
	for(int i = 0; i < alts; i++) {
		uint8_t altQ = altQual[i][off]; // qual of alt call
		if(altQ == 33) break; // no alt call
		assert_leq(altQ, primQ);
		uint8_t pen = roundPenalty(primQ - altQ);
		if(pen < bestPenalty) {
			bestPenalty = pen;
		}
		// Get the base
		int altC = (int)altQry[i][off];
		assert_lt(altC, 4);
		q[altC] = pen;
	}
	// Return the best penalty so that the caller can evaluate whether
	// any of the penalties are within-budget
	return bestPenalty;
}

/**
 * Fill the q[] array with the penalties that are determined by
 * subtracting the quality values of the alternate basecalls from
 * the quality of the primary basecall.
 */
inline static uint8_t loPenaltyAt(size_t off, int alts,
                                  const BTString&    qual,
                                  const BTString    *altQual)
{
	uint8_t primQ = qual[off]; // qual of primary call
	uint8_t bestPenalty = roundPenalty(phredcToPhredq(primQ));
	for(int i = 0; i < alts; i++) {
		uint8_t altQ = altQual[i][off]; // qual of alt call
		if(altQ == 33) break; // no more alt calls at this position
		assert_leq(altQ, primQ);
		uint8_t pen = roundPenalty(primQ - altQ);
		if(pen < bestPenalty) {
			bestPenalty = pen;
		}
	}
	return bestPenalty;
}

#endif /*QUAL_H_*/