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Output.c
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Output.c
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/*
* 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.
*/
/*
Authors:
Farhad Hormozdiari
Faraz Hach
Emails:
farhadh AT uw DOT edu
fhach AT cs DOT sfu
*/
#include <stdio.h>
#include <stdlib.h>
#include <zlib.h>
#include <string.h>
#include "Common.h"
#include "Output.h"
FILE *_out_fp;
gzFile _out_gzfp;
char buffer[300000];
int bufferSize = 0;
void finalizeGZOutput()
{
gzclose(_out_gzfp);
}
void finalizeTXOutput()
{
fclose(_out_fp);
}
void gzOutputQ(SAM map)
{
gzprintf(_out_gzfp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
map.QNAME,
map.FLAG,
map.RNAME,
map.POS,
map.MAPQ,
map.CIGAR,
map.MRNAME,
map.MPOS,
map.ISIZE,
map.SEQ,
map.QUAL);
int i;
for ( i = 0; i < map.optSize; i++)
{
switch (map.optFields[i].type)
{
case 'A':
gzprintf(_out_gzfp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
break;
case 'i':
gzprintf(_out_gzfp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
break;
case 'f':
gzprintf(_out_gzfp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
break;
case 'Z':
case 'H':
gzprintf(_out_gzfp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
break;
}
}
gzprintf(_out_gzfp, "\n");
}
void outputSAM(FILE *fp, SAM map)
{
fprintf(fp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
map.QNAME,
map.FLAG,
map.RNAME,
map.POS,
map.MAPQ,
map.CIGAR,
map.MRNAME,
map.MPOS,
map.ISIZE,
map.SEQ,
map.QUAL);
int i;
for ( i = 0; i < map.optSize; i++)
{
switch (map.optFields[i].type)
{
case 'A':
fprintf(fp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
break;
case 'i':
fprintf(fp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
break;
case 'f':
fprintf(fp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
break;
case 'Z':
case 'H':
fprintf(fp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
break;
}
}
fprintf(fp, "\n");
}
void outputQ(SAM map)
{
fprintf(_out_fp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
map.QNAME,
map.FLAG,
map.RNAME,
map.POS,
map.MAPQ,
map.CIGAR,
map.MRNAME,
map.MPOS,
map.ISIZE,
map.SEQ,
map.QUAL);
int i;
for ( i = 0; i < map.optSize; i++)
{
switch (map.optFields[i].type)
{
case 'A':
fprintf(_out_fp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
break;
case 'i':
fprintf(_out_fp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
break;
case 'f':
fprintf(_out_fp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
break;
case 'Z':
case 'H':
fprintf(_out_fp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
break;
}
}
fprintf(_out_fp, "\n");
}
int initOutput ( char *fileName, int compressed)
{
if (compressed)
{
char newFileName[strlen(fileName)+4];
sprintf(newFileName, "%s.gz", fileName);
_out_gzfp = fileOpenGZ(newFileName, "w1f");
if (_out_gzfp == Z_NULL)
{
return 0;
}
finalizeOutput = &finalizeGZOutput;
output = &gzOutputQ;
}
else
{
_out_fp = fileOpen(fileName, "w");
if (_out_fp == NULL)
{
return 0;
}
finalizeOutput = &finalizeTXOutput;
output = &outputQ;
}
buffer[0] = '\0';
return 1;
}
FILE* getOutputFILE()
{
if(_out_fp != NULL)
return _out_fp;
else if(_out_gzfp != NULL)
return _out_gzfp;
else
return NULL;
}