hisat-3n/ref_read.h

/*
 * 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 REF_READ_H_
#define REF_READ_H_

#include <iostream>
#include <cassert>
#include <string>
#include <ctype.h>
#include <fstream>
#include <stdexcept>
#include "alphabet.h"
#include "assert_helpers.h"
#include "filebuf.h"
#include "word_io.h"
#include "ds.h"
#include "endian_swap.h"

using namespace std;

class RefTooLongException : public exception {

public:
	RefTooLongException() {
#ifdef BOWTIE_64BIT_INDEX
		// This should never happen!
		msg = "Error: Reference sequence has more than 2^64-1 characters!  "
		      "Please divide the reference into smaller chunks and index each "
			  "independently.";
#else
		msg = "Error: Reference sequence has more than 2^32-1 characters!  "
		      "Please build a large index by passing the --large-index option "
			  "to bowtie2-build";
#endif
	}
	
	~RefTooLongException() throw() {}
	
	const char* what() const throw() {
		return msg.c_str();
	}

protected:
	
	string msg;
	
};

/**
 * Encapsulates a stretch of the reference containing only unambiguous
 * characters.  From an ordered list of RefRecords, one can (almost)
 * deduce the "shape" of the reference sequences (almost because we
 * lose information about stretches of ambiguous characters at the end
 * of reference sequences).
 */
struct RefRecord {
	RefRecord() : off(), len(), first() { }
	RefRecord(TIndexOffU _off, TIndexOffU _len, bool _first) :
		off(_off), len(_len), first(_first)
	{ }

	RefRecord(FILE *in, bool swap) {
		assert(in != NULL);
		if(!fread(&off, OFF_SIZE, 1, in)) {
			cerr << "Error reading RefRecord offset from FILE" << endl;
			throw 1;
		}
		if(swap) off = endianSwapIndex(off);
		if(!fread(&len, OFF_SIZE, 1, in)) {
			cerr << "Error reading RefRecord offset from FILE" << endl;
			throw 1;
		}
		if(swap) len = endianSwapIndex(len);
		first = fgetc(in) ? true : false;
	}

	void write(std::ostream& out, bool be) {
		writeIndex<TIndexOffU>(out, off, be);
		writeIndex<TIndexOffU>(out, len, be);
		out.put(first ? 1 : 0);
	}

	TIndexOffU off; /// Offset of the first character in the record
	TIndexOffU len; /// Length of the record
	bool   first; /// Whether this record is the first for a reference sequence
};

enum {
	REF_READ_FORWARD = 0, // don't reverse reference sequence
	REF_READ_REVERSE,     // reverse entire reference sequence
	REF_READ_REVERSE_EACH, // reverse each unambiguous stretch of reference
    REF_READ_REVERSE_REPLACEMENT, // reverse the entire reference sequence and replace specific base by others.
};

/**
 * Parameters governing treatment of references as they're read in.
 */
struct RefReadInParams {
	RefReadInParams(bool col, int r, bool nsToA, bool bisulf) :
		color(col), reverse(r), nsToAs(nsToA), bisulfite(bisulf) { }
	// extract colors from reference
	bool color;
	// reverse each reference sequence before passing it along
	int reverse;
	// convert ambiguous characters to As
	bool nsToAs;
	// bisulfite-convert the reference
	bool bisulfite;
};

extern RefRecord
fastaRefReadSize(
	FileBuf& in,
	const RefReadInParams& rparms,
	bool first,
	BitpairOutFileBuf* bpout,
	string *name = NULL);

extern std::pair<size_t, size_t>
fastaRefReadSizes(
	EList<FileBuf*>& in,
	EList<RefRecord>& recs,
	const RefReadInParams& rparms,
	BitpairOutFileBuf* bpout,
	TIndexOff& numSeqs);

extern std::pair<size_t, size_t>
fastaRefReadFragsNames(
	EList<FileBuf*>& in,
	EList<RefRecord>& recs,
	const RefReadInParams& rparms,
	BitpairOutFileBuf* bpout,
	TIndexOff& numSeqs,
	EList<string>& names);

extern void
reverseRefRecords(
	const EList<RefRecord>& src,
	EList<RefRecord>& dst,
	bool recursive = false,
	bool verbose = false);

/**
 * Reads the next sequence from the given FASTA file and appends it to
 * the end of dst, optionally reversing it.
 */
template <typename TStr>
static RefRecord fastaRefReadAppend(
	FileBuf& in,             // input file
	bool first,              // true iff this is the first record in the file
	TStr& dst,               // destination buf for parsed characters
	TIndexOffU& dstoff,          // index of next character in dst to assign
	RefReadInParams& rparms, // 
	string* name = NULL)     // put parsed FASTA name here
{
	int c;
	static int lastc = '>';
	if(first) {
		c = in.getPastWhitespace();
		if(c != '>') {
			cerr << "Reference file does not seem to be a FASTA file" << endl;
			throw 1;
		}
		lastc = c;
	}
	assert_neq(-1, lastc);

	// RefRecord params
	size_t len = 0;
	size_t off = 0;
	first = true;

	size_t ilen = dstoff;

	// Chew up the id line; if the next line is either
	// another id line or a comment line, keep chewing
	int lc = -1; // last-DNA char variable for color conversion
	c = lastc;
	if(c == '>' || c == '#') {
		do {
			while (c == '#') {
				if((c = in.getPastNewline()) == -1) {
					lastc = -1;
					goto bail;
				}
			}
			assert_eq('>', c);
			while(true) {
				c = in.get();
				if(c == -1) {
					lastc = -1;
					goto bail;
				}
				if(c == '\n' || c == '\r') {
					while(c == '\r' || c == '\n') c = in.get();
					if(c == -1) {
						lastc = -1;
						goto bail;
					}
					break;
				}
				if (name) name->push_back(c);
			}
			// c holds the first character on the line after the name
			// line
			if(c == '>') {
				// If there's another name line immediately after this one,
				// discard the previous name and start fresh with the new one
				if (name) name->clear();
			}
		} while (c == '>' || c == '#');
	} else {
		ASSERT_ONLY(int cc = toupper(c));
		assert(cc != 'A' && cc != 'C' && cc != 'G' && cc != 'T');
		first = false;
	}

	// Skip over an initial stretch of gaps or ambiguous characters.
	// For colorspace we skip until we see two consecutive unambiguous
	// characters (i.e. the first unambiguous color).
	while(true) {
		int cat = asc2dnacat[c];
		if(rparms.nsToAs && cat >= 2) {
			c = 'A';
		}
		int cc = toupper(c);
		if(rparms.bisulfite && cc == 'C') c = cc = 'T';
		if(cat == 1) {
			// This is a DNA character
			if(rparms.color) {
				if(lc != -1) {
					// Got two consecutive unambiguous DNAs
					break; // to read-in loop
				}
				// Keep going; we need two consecutive unambiguous DNAs
				lc = asc2dna[(int)c];
				// The 'if(off > 0)' takes care of the case where
				// the reference is entirely unambiguous and we don't
				// want to incorrectly increment off.
				if(off > 0) off++;
			} else {
				break; // to read-in loop
			}
		} else if(cat >= 2) {
			if(lc != -1 && off == 0) {
				off++;
			}
			lc = -1;
			off++; // skip it
		} else if(c == '>') {
			lastc = '>';
			goto bail;
		}
		c = in.get();
		if(c == -1) {
			lastc = -1;
			goto bail;
		}
	}
	if(first && rparms.color && off > 0) {
		// Handle the case where the first record has ambiguous
		// characters but we're in color space; one of those counts is
		// spurious
		off--;
	}
	assert(!rparms.color || lc != -1);
	assert_eq(1, asc2dnacat[c]);

	// in now points just past the first character of a sequence
	// line, and c holds the first character
	while(true) {
		// Note: can't have a comment in the middle of a sequence,
		// though a comment can end a sequence
		int cat = asc2dnacat[c];
		assert_neq(2, cat);
		if(cat == 1) {
			// Consume it
			if(!rparms.color || lc != -1) len++;
			// Add it to reference buffer
			if(rparms.color) {
				dst.set((char)dinuc2color[asc2dna[(int)c]][lc], dstoff++);
			} else if(!rparms.color) {
				dst.set(asc2dna[c], dstoff++);
			}
			assert_lt((int)dst[dstoff-1], 4);
			lc = asc2dna[(int)c];
		}
		c = in.get();
		if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A';
		if (c == -1 || c == '>' || c == '#' || asc2dnacat[c] >= 2) {
			lastc = c;
			break;
		}
		if(rparms.bisulfite && toupper(c) == 'C') c = 'T';
	}

  bail:
	// Optionally reverse the portion that we just appended.
	// ilen = length of buffer before this last sequence was appended.
	if(rparms.reverse == REF_READ_REVERSE_EACH) {
		// Find limits of the portion we just appended
		size_t nlen = dstoff;
		dst.reverseWindow(ilen, nlen);
	}
	return RefRecord((TIndexOffU)off, (TIndexOffU)len, first);
}

#endif /*ndef REF_READ_H_*/