edit.h 8.04 KB
Newer Older
1
/*
2
 * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
 *
 * 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 EDIT_H_
#define EDIT_H_

#include <iostream>
#include <stdint.h>
25
#include <limits>
26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42
#include "assert_helpers.h"
#include "filebuf.h"
#include "sstring.h"
#include "ds.h"

/**
 * 3 types of edits; mismatch (substitution), insertion in the
 * reference, deletion in the reference.
 */
enum {
	EDIT_TYPE_READ_GAP = 1,
	EDIT_TYPE_REF_GAP,
	EDIT_TYPE_MM,
	EDIT_TYPE_SNP
};

/**
43 44 45 46 47 48 49 50 51 52 53 54 55 56
 * Encapsulates an edit between the read sequence and the reference sequence.
 * We obey a few conventions when populating its fields.  The fields are:
 *
 * 	uint8_t  chr;  // reference character involved (for subst and ins)
 *  uint8_t  qchr; // read character involved (for subst and del)
 *  uint8_t  type; // 1 -> mm, 2 -> SNP, 3 -> ins, 4 -> del
 *  uint32_t pos;  // position w/r/t search root
 *
 * One convention is that pos is always an offset w/r/t the 5' end of the read.
 *
 * Another is that chr and qchr are expressed in terms of the nucleotides on
 * the forward version of the read.  So if we're aligning the reverse
 * complement of the read, and an A in the reverse complement mismatches a C in
 * the reference, chr should be G and qchr should be T.
57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
 */
struct Edit {

	Edit() { reset(); }

	Edit(
		uint32_t po,
		int ch,
		int qc,
		int ty,
		bool chrs = true)
	{
		init(po, ch, qc, ty, chrs);
	}
	
72 73 74
    /**
     * Reset Edit to uninitialized state.
     */
75
	void reset() {
76 77
		pos = pos2 = std::numeric_limits<uint32_t>::max();
		chr = qchr = type = 0;
78 79
	}
	
80 81 82
    /**
     * Return true iff the Edit is initialized.
     */
83
	bool inited() const {
84
		return pos != std::numeric_limits<uint32_t>::max();
85 86
	}
	
87 88 89
    /**
     * Initialize a new Edit.
     */
90 91 92 93 94 95 96 97 98 99 100
	void init(
		uint32_t po,
		int ch,
		int qc,
		int ty,
		bool chrs = true)
	{
		chr = ch;
		qchr = qc;
		type = ty;
		pos = po;
101 102 103 104 105 106
		if(qc == '-') {
			// Read gap
			pos2 = std::numeric_limits<uint32_t>::max() >> 1;
		} else {
			pos2 = std::numeric_limits<uint32_t>::max();
		}
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
		if(!chrs) {
			assert_range(0, 4, (int)chr);
			assert_range(0, 4, (int)qchr);
			chr = "ACGTN"[chr];
			qchr = "ACGTN"[qchr];
		}
		assert_in(chr, "ACMGRSVTWYHKDBN-");
		assert_in(qchr, "ACGTN-");
		assert(chr != qchr || chr == 'N');
		assert(inited());
	}
	
	/**
	 * Return true iff one part of the edit or the other has an 'N'.
	 */
	bool hasN() const {
		assert(inited());
		return chr == 'N' || qchr == 'N';
	}

	/**
	 * Edit less-than overload.
	 */
	int operator< (const Edit &rhs) const {
		assert(inited());
		if(pos  < rhs.pos) return 1;
		if(pos  > rhs.pos) return 0;
134 135
		if(pos2 < rhs.pos2) return 1;
		if(pos2 > rhs.pos2) return 0;
136 137 138 139 140 141 142 143 144 145 146 147 148
		if(type < rhs.type) return 1;
		if(type > rhs.type) return 0;
		if(chr  < rhs.chr) return 1;
		if(chr  > rhs.chr) return 0;
		return (qchr < rhs.qchr)? 1 : 0;
	}

	/**
	 * Edit equals overload.
	 */
	int operator== (const Edit &rhs) const {
		assert(inited());
		return(pos  == rhs.pos &&
149
			   pos2 == rhs.pos2 &&
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
			   chr  == rhs.chr &&
			   qchr == rhs.qchr &&
			   type == rhs.type);
	}

	/**
	 * Return true iff this Edit is an initialized insertion.
	 */
	bool isReadGap() const {
		assert(inited());
		return type == EDIT_TYPE_READ_GAP;
	}

	/**
	 * Return true iff this Edit is an initialized deletion.
	 */
	bool isRefGap() const {
		assert(inited());
		return type == EDIT_TYPE_REF_GAP;
	}

	/**
	 * Return true if this Edit is either an initialized deletion or an
	 * initialized insertion.
	 */
	bool isGap() const {
		assert(inited());
		return (type == EDIT_TYPE_REF_GAP || type == EDIT_TYPE_READ_GAP);
	}
	
	/**
	 * Return the number of gaps in the given edit list.
	 */
	static size_t numGaps(const EList<Edit>& es) {
		size_t gaps = 0;
		for(size_t i = 0; i < es.size(); i++) {
			if(es[i].isGap()) gaps++;
		}
		return gaps;
	}

	/**
	 * Return true iff this Edit is an initialized mismatch.
	 */
	bool isMismatch() const {
		assert(inited());
		return type == EDIT_TYPE_MM;
	}

	/**
	 * Sort the edits in the provided list.
	 */
	static void sort(EList<Edit>& edits);

	/**
	 * Flip all the edits.pos fields so that they're with respect to
	 * the other end of the read (of length 'sz').
	 */
208 209 210 211 212 213
	static void invertPoss(
		EList<Edit>& edits,
		size_t sz,
		size_t ei,
		size_t en,
		bool sort = false);
214 215 216 217 218

	/**
	 * Flip all the edits.pos fields so that they're with respect to
	 * the other end of the read (of length 'sz').
	 */
219 220
	static void invertPoss(EList<Edit>& edits, size_t sz, bool sort = false) {
		invertPoss(edits, sz, 0, edits.size(), sort);
221
	}
222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288
	
	/**
	 * Clip off some of the low-numbered positions.
	 */
	static void clipLo(EList<Edit>& edits, size_t len, size_t amt);

	/**
	 * Clip off some of the high-numbered positions.
	 */
	static void clipHi(EList<Edit>& edits, size_t len, size_t amt);

	/**
	 * Given a read string and some edits, generate and append the
	 * corresponding reference string to 'ref'.
	 */
	static void toRef(
		const BTDnaString& read,
		const EList<Edit>& edits,
		BTDnaString& ref,
		bool fw = true,
		size_t trim5 = 0,
		size_t trim3 = 0);

	/**
	 * Given a string and its edits with respect to some other string,
	 * print the alignment between the strings with the strings stacked
	 * vertically, with vertical bars denoting matches.
	 */
	static void printQAlign(
		std::ostream& os,
		const BTDnaString& read,
		const EList<Edit>& edits);

	/**
	 * Given a string and its edits with respect to some other string,
	 * print the alignment between the strings with the strings stacked
	 * vertically, with vertical bars denoting matches.  Add 'prefix'
	 * before each line of output.
	 */
	static void printQAlign(
		std::ostream& os,
		const char *prefix,
		const BTDnaString& read,
		const EList<Edit>& edits);

	/**
	 * Given a string and its edits with respect to some other string,
	 * print the alignment between the strings with the strings stacked
	 * vertically, with vertical bars denoting matches.
	 */
	static void printQAlignNoCheck(
		std::ostream& os,
		const BTDnaString& read,
		const EList<Edit>& edits);

	/**
	 * Given a string and its edits with respect to some other string,
	 * print the alignment between the strings with the strings stacked
	 * vertically, with vertical bars denoting matches.  Add 'prefix'
	 * before each line of output.
	 */
	static void printQAlignNoCheck(
		std::ostream& os,
		const char *prefix,
		const BTDnaString& read,
		const EList<Edit>& edits);

289
#ifndef NDEBUG
290 291 292 293 294 295 296 297 298 299 300 301 302
	bool repOk() const;

	/**
	 * Given a list of edits and a DNA string representing the query
	 * sequence, check that the edits are consistent with respect to the
	 * query.
	 */
	static bool repOk(
		const EList<Edit>& edits,
		const BTDnaString& s,
		bool fw = true,
		size_t trim5 = 0,
		size_t trim3 = 0);
303
#endif
304 305 306 307 308

	uint8_t  chr;  // reference character involved (for subst and ins)
	uint8_t  qchr; // read character involved (for subst and del)
	uint8_t  type; // 1 -> mm, 2 -> SNP, 3 -> ins, 4 -> del
	uint32_t pos;  // position w/r/t search root
309 310 311
	uint32_t pos2; // Second int to take into account when sorting.  Useful for
	               // sorting read gap edits that are all part of the same long
				   // gap.
312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330

	friend std::ostream& operator<< (std::ostream& os, const Edit& e);

	/**
	 * Print a comma-separated list of Edits to given output stream.
	 */
	static void print(
		std::ostream& os,
		const EList<Edit>& edits,
		char delim = '\t');

	/**
	 * Merge second argument into the first.  Assume both are sorted to
	 * begin with.
	 */
	static void merge(EList<Edit>& dst, const EList<Edit>& src);
};

#endif /* EDIT_H_ */