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comparison mrsfast-2.3.0.2/Output.c @ 0:ec628ba33878 default tip

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Uploaded source code for mrsFAST
author calkan
date Tue, 21 Feb 2012 10:39:28 -0500
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-1:000000000000 0:ec628ba33878
1 /*
2 * Copyright (c) <2008 - 2009>, University of Washington, Simon Fraser University
3 * All rights reserved.
4 *
5 * Redistribution and use in source and binary forms, with or without modification,
6 * are permitted provided that the following conditions are met:
7 *
8 * Redistributions of source code must retain the above copyright notice, this list
9 * of conditions and the following disclaimer.
10 * - Redistributions in binary form must reproduce the above copyright notice, this
11 * list of conditions and the following disclaimer in the documentation and/or other
12 * materials provided with the distribution.
13 * - Neither the name of the <ORGANIZATION> nor the names of its contributors may be
14 * used to endorse or promote products derived from this software without specific
15 * prior written permission.
16 *
17 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
18 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
19 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
20 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
21 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
22 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
23 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
24 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
25 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
26 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
27 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
28 */
29
30 /*
31 * Author : Faraz Hach
32 * Email : fhach AT cs DOT sfu
33 * Last Update : 2009-12-08
34 */
35
36
37 #include <stdio.h>
38 #include <stdlib.h>
39 #include <zlib.h>
40 #include <string.h>
41 #include "Common.h"
42 #include "Output.h"
43
44 FILE *_out_fp;
45 gzFile _out_gzfp;
46
47
48
49 void finalizeGZOutput()
50 {
51 gzclose(_out_gzfp);
52 }
53
54 void finalizeTXOutput()
55 {
56 fclose(_out_fp);
57 }
58
59
60 void gzOutputQ(SAM map)
61 {
62 gzprintf(_out_gzfp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
63 map.QNAME,
64 map.FLAG,
65 map.RNAME,
66 map.POS,
67 map.MAPQ,
68 map.CIGAR,
69 map.MRNAME,
70 map.MPOS,
71 map.ISIZE,
72 map.SEQ,
73 map.QUAL);
74
75 int i;
76
77 for ( i = 0; i < map.optSize; i++)
78 {
79 switch (map.optFields[i].type)
80 {
81 case 'A':
82 gzprintf(_out_gzfp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
83 break;
84 case 'i':
85 gzprintf(_out_gzfp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
86 break;
87 case 'f':
88 gzprintf(_out_gzfp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
89 break;
90 case 'Z':
91 case 'H':
92 gzprintf(_out_gzfp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
93 break;
94 }
95 }
96 gzprintf(_out_gzfp, "\n");
97 }
98
99 void outputQ(SAM map)
100 {
101
102 fprintf(_out_fp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
103 map.QNAME,
104 map.FLAG,
105 map.RNAME,
106 map.POS,
107 map.MAPQ,
108 map.CIGAR,
109 map.MRNAME,
110 map.MPOS,
111 map.ISIZE,
112 map.SEQ,
113 map.QUAL);
114
115
116 int i;
117
118 for ( i = 0; i < map.optSize; i++)
119 {
120 switch (map.optFields[i].type)
121 {
122 case 'A':
123 fprintf(_out_fp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
124 break;
125 case 'i':
126 fprintf(_out_fp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
127 break;
128 case 'f':
129 fprintf(_out_fp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
130 break;
131 case 'Z':
132 case 'H':
133 fprintf(_out_fp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
134 break;
135 }
136 }
137
138 fprintf(_out_fp, "\n");
139 }
140
141 int initOutput ( char *fileName, int compressed)
142 {
143 if (compressed)
144 {
145 char newFileName[strlen(mappingOutputPath)+strlen(fileName)+4];
146 sprintf(newFileName, "%s%s.gz", mappingOutputPath, fileName);
147 _out_gzfp = fileOpenGZ(newFileName, "w1f");
148 if (_out_gzfp == Z_NULL)
149 {
150 return 0;
151 }
152
153 finalizeOutput = &finalizeGZOutput;
154
155 output = &gzOutputQ;
156 }
157 else
158 {
159
160 char newFileName[strlen(mappingOutputPath)+strlen(fileName)];
161 sprintf(newFileName, "%s%s", mappingOutputPath, fileName);
162
163 _out_fp = fileOpen(newFileName, "w");
164 if (_out_fp == NULL)
165 {
166 return 0;
167 }
168
169 finalizeOutput = &finalizeTXOutput;
170 output = &outputQ;
171 }
172 return 1;
173 }
174
175