Output.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.
 */

/*
  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;
}