https://github.com/sfu-compbio/mrsfast
Tip revision: 2e121b244f48d1522425eb6029e5952a31824f3d authored by Faraz Hach on 13 June 2012, 07:23:00 UTC
Version 1.1.6.2
Version 1.1.6.2
Tip revision: 2e121b2
RefGenome.c
/*
* Copyright (c) <2008 - 2009>, 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.
*/
#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;
/**********************************************/
int initLoadingRefGenome(char *fileName)
{
char ch;
_rg_fp = fileOpen (fileName, "r");
if (fscanf(_rg_fp, "%c", &ch))
{
if (ch == '>')
{
_rg_contGen = 0;
_rg_offset = 0;
_rg_gen = getMem(CONTIG_MAX_SIZE);
_rg_name = getMem(CONTIG_NAME_SIZE);
return 1;
}
}
return 0;
}
/**********************************************/
void finalizeLoadingRefGenome()
{
freeMem(_rg_gen, CONTIG_MAX_SIZE);
freeMem(_rg_name, CONTIG_NAME_SIZE);
fclose(_rg_fp);
}
/**********************************************/
int loadRefGenome(char **refGen, char **refGenName, int *refGenOff)
{
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);
}
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 = 1;
break;
}
else if (!isspace(ch))
{
ch = toupper(ch);
_rg_gen[size++] = ch;
if (ch != 'N')
{
actualSize++;
}
if (actualSize == CONTIG__SIZE || size == CONTIG_MAX_SIZE)
{
_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;
}
return returnVal;
}
/**********************************************/