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comparison mrfast-2.1.0.5/Output.c @ 1:d4054b05b015 default tip

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Version update to 2.1.0.5
author calkan
date Fri, 09 Mar 2012 07:35:51 -0500
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0:7b3dc85dc7fd 1:d4054b05b015
1 /*
2 * Copyright (c) <2008 - 2012>, 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 names of the University of Washington, Simon Fraser University,
14 * nor the names of its contributors may be
15 * used to endorse or promote products derived from this software without specific
16 * prior written permission.
17 *
18 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
19 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
20 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
21 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
22 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
25 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
26 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
27 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
28 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 */
30
31 /*
32 Authors:
33 Farhad Hormozdiari
34 Faraz Hach
35 Can Alkan
36 Emails:
37 farhadh AT uw DOT edu
38 fhach AT cs DOT sfu DOT ca
39 calkan AT uw DOT edu
40 */
41
42
43 #include <stdio.h>
44 #include <stdlib.h>
45 #include <zlib.h>
46 #include <string.h>
47 #include "Common.h"
48 #include "Output.h"
49
50 FILE *_out_fp;
51 gzFile _out_gzfp;
52
53 char buffer[300000];
54 int bufferSize = 0;
55
56
57 void finalizeGZOutput()
58 {
59 gzclose(_out_gzfp);
60 }
61
62 void finalizeTXOutput()
63 {
64 fclose(_out_fp);
65 }
66
67
68 void gzOutputQ(SAM map)
69 {
70 gzprintf(_out_gzfp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
71 map.QNAME,
72 map.FLAG,
73 map.RNAME,
74 map.POS,
75 map.MAPQ,
76 map.CIGAR,
77 map.MRNAME,
78 map.MPOS,
79 map.ISIZE,
80 map.SEQ,
81 map.QUAL);
82
83 int i;
84
85 for ( i = 0; i < map.optSize; i++)
86 {
87 switch (map.optFields[i].type)
88 {
89 case 'A':
90 gzprintf(_out_gzfp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
91 break;
92 case 'i':
93 gzprintf(_out_gzfp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
94 break;
95 case 'f':
96 gzprintf(_out_gzfp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
97 break;
98 case 'Z':
99 case 'H':
100 gzprintf(_out_gzfp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
101 break;
102 }
103 }
104 gzprintf(_out_gzfp, "\n");
105 }
106
107 void outputSAM(FILE *fp, SAM map)
108 {
109 fprintf(fp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
110 map.QNAME,
111 map.FLAG,
112 map.RNAME,
113 map.POS,
114 map.MAPQ,
115 map.CIGAR,
116 map.MRNAME,
117 map.MPOS,
118 map.ISIZE,
119 map.SEQ,
120 map.QUAL);
121
122
123 int i;
124
125 for ( i = 0; i < map.optSize; i++)
126 {
127 switch (map.optFields[i].type)
128 {
129 case 'A':
130 fprintf(fp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
131 break;
132 case 'i':
133 fprintf(fp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
134 break;
135 case 'f':
136 fprintf(fp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
137 break;
138 case 'Z':
139 case 'H':
140 fprintf(fp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
141 break;
142 }
143 }
144
145 fprintf(fp, "\n");
146
147 }
148
149 void outputQ(SAM map)
150 {
151
152 fprintf(_out_fp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
153 map.QNAME,
154 map.FLAG,
155 map.RNAME,
156 map.POS,
157 map.MAPQ,
158 map.CIGAR,
159 map.MRNAME,
160 map.MPOS,
161 map.ISIZE,
162 map.SEQ,
163 map.QUAL);
164
165
166 int i;
167
168 for ( i = 0; i < map.optSize; i++)
169 {
170 switch (map.optFields[i].type)
171 {
172 case 'A':
173 fprintf(_out_fp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
174 break;
175 case 'i':
176 fprintf(_out_fp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
177 break;
178 case 'f':
179 fprintf(_out_fp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
180 break;
181 case 'Z':
182 case 'H':
183 fprintf(_out_fp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
184 break;
185 }
186 }
187
188 fprintf(_out_fp, "\n");
189 }
190
191 int initOutput ( char *fileName, int compressed)
192 {
193 if (compressed)
194 {
195 char newFileName[strlen(fileName)+4];
196 sprintf(newFileName, "%s.gz", fileName);
197
198 _out_gzfp = fileOpenGZ(newFileName, "w1f");
199 if (_out_gzfp == Z_NULL)
200 {
201 return 0;
202 }
203
204 finalizeOutput = &finalizeGZOutput;
205
206 output = &gzOutputQ;
207 }
208 else
209 {
210 _out_fp = fileOpen(fileName, "w");
211 if (_out_fp == NULL)
212 {
213 return 0;
214 }
215
216 finalizeOutput = &finalizeTXOutput;
217 output = &outputQ;
218 }
219 buffer[0] = '\0';
220 return 1;
221 }
222
223 FILE* getOutputFILE()
224 {
225 if(_out_fp != NULL)
226 return _out_fp;
227 else if(_out_gzfp != NULL)
228 return _out_gzfp;
229 else
230 return NULL;
231 }