--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mrfast-2.1.0.4/Output.c	Tue Feb 21 10:29:47 2012 -0500
@@ -0,0 +1,231 @@
+/*
+ * Copyright (c) <2008 - 2012>, 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 names of the University of Washington, Simon Fraser University, 
+ *   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
+	Can Alkan
+  Emails: 
+	farhadh AT uw DOT edu
+	fhach AT cs DOT sfu DOT ca
+        calkan AT uw DOT edu
+*/
+
+
+#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;
+}