RefGenome.c

/*
 * Copyright (c) <2008 - 2020>, University of Washington, Simon Fraser University
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without modification, 
 * are permitted provided that the following conditions are met:
 *   
 * Redistributions of source code must retain the above copyright notice, this list
 * of conditions and the following disclaimer.
 * - 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.
 * - Neither the name of the <ORGANIZATION> 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 THE COPYRIGHT HOLDERS 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 THE COPYRIGHT OWNER 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: 
 *        Faraz Hach (fhach AT cs DOT sfu DOT ca)
 *        Iman Sarrafi (isarrafi AT cs DOT sfu DOT ca)
 */


#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "Common.h"
#include "RefGenome.h"

FILE *_rg_fp;
char *_rg_gen;
char *_rg_name;
int _rg_offset;
int _rg_contGen;		// false if this segment is the first contig

int getGenomeMetaInfo(char*, char*, int*);

/**********************************************/
int initLoadingRefGenome(char *fileName, char *genomeMetaInfo, int *genomeMetaInfoLength)
{
	_rg_fp = fileOpen (fileName, "r");
	
	if (!getGenomeMetaInfo(fileName, genomeMetaInfo, genomeMetaInfoLength))
		return 0;

	char ch;
	fscanf(_rg_fp, "%c", &ch);		// '>'
	_rg_contGen = 0;
	_rg_offset = 0;
	_rg_gen = getMem(CONTIG_MAX_SIZE + 21);
	_rg_name = getMem(CONTIG_NAME_SIZE);
	return 1;
}
/**********************************************/
void finalizeLoadingRefGenome()
{
	freeMem(_rg_gen, CONTIG_MAX_SIZE + 21);
	freeMem(_rg_name, CONTIG_NAME_SIZE); 
	fclose(_rg_fp);
}
/**********************************************/
int loadRefGenome(char **refGen, char **refGenName, int *refGenOff, int *refGenLen)
{
	char ch;
	int i;
	int returnVal = 0;
	int actualSize=0;
	int size;
	char *tmp;

	// New Conting 
	if (!_rg_contGen)
	{
		size = 0;
		tmp = fgets(_rg_name, SEQ_MAX_LENGTH, _rg_fp);
		int k;
		for (k=0; _rg_name[k] != '\0';k++)
		{
			if (_rg_name[k] == ' ' || _rg_name[k] == '\t')
			{
				_rg_name[k]='\0';
				break;
			}
		}

	}
	else
	{
		size=strlen(_rg_gen);
		for( i = 0 ; i < CONTIG_OVERLAP ; i++ )
		{
			_rg_gen[i] = _rg_gen[size-CONTIG_OVERLAP+i];
			if (_rg_gen[i] != 'N')
				actualSize++;
		}
		size = CONTIG_OVERLAP;
	}

	while( fscanf(_rg_fp, "%c", &ch) > 0 )
	{
		if (ch == '>')
		{
			_rg_contGen = 0;
			returnVal = 2;
			break;
		}
		else if (!isspace(ch))
		{
			ch = toupper(ch);
			_rg_gen[size++] = ch;
			if (ch != 'N')
			{
				actualSize++;
			}
			if ((actualSize > CONTIG_SIZE || size >= CONTIG_MAX_SIZE) && size%21 == 0)
			{
				_rg_contGen = 1;
				returnVal=1;
				break;
			}
		}

	}

	_rg_gen[size] = '\0';
	for (i=strlen(_rg_name)-1; i >= 0; i--)
		if (!isspace(_rg_name[i]))
			break;
	_rg_name[i+1] = '\0';

	*refGenOff = _rg_offset;
	*refGenName = _rg_name;
	*refGen = _rg_gen;

	if (_rg_contGen == 1)
	{
		_rg_offset += size-CONTIG_OVERLAP;
	}
	else
	{
		_rg_offset = 0;
	}

	*refGenLen = size;
	return returnVal;
}
/**********************************************/
int getGenomeMetaInfo(char *fileName, char *genomeMetaInfo, int *genomeMetaInfoLength)
{
	// genomeMetaInfo structure:
	// 4 bytes (numOfChrs): number of chromosomes in file
	// for each chromosome we have the following
	// 4 bytes (nameLen): length of the chromosome name
	// n bytes (name): chromosome name
	// 4 bytes (genSize): length of the chromosome in characters
	
	char ch, *tmp;
	int *nameLen, *genSize, *numOfChrs = (int *)genomeMetaInfo;
	*numOfChrs = 0;
	int i = sizeof(int);

	if ( fscanf(_rg_fp, "%c", &ch) > 0 )
	{
		if (ch != '>')
		{
			fprintf(stdout, "Error: Wrong fasta format file\n");
			return 0;
		}
	}
	else
		return 0;

	rewind(_rg_fp);

	fprintf(stdout, "Scanning the fasta file: ");
	while( fscanf(_rg_fp, "%c", &ch) > 0 )
	{
		if (!isspace(ch))
		{
			if (ch == '>')
			{
				(*numOfChrs)++;
				nameLen = (int *)(genomeMetaInfo + i);
				*nameLen = 0;
				i += sizeof(int);
				tmp = fgets(genomeMetaInfo + i, SEQ_MAX_LENGTH, _rg_fp);
				while(!isspace(*(genomeMetaInfo+i)))
				{
					i++;
					(*nameLen)++;
				}
				genSize = (int *)(genomeMetaInfo + i);
				i += sizeof(int);
				*genSize = 0;
				fprintf(stdout, ".");
				fflush(stdout);
			}
			else
			{
				(*genSize)++;
			}
		}
	}
	fprintf(stdout, "\n");
	*genomeMetaInfoLength = i;

	rewind(_rg_fp);
	return 1;
}