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comparison mrfast-2.1.0.5/Output.h @ 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
44 #ifndef __OUTPUT__
45 #define __OUTPUT__
46
47 #define FORWARD 0
48 #define REVERSE 1
49
50 typedef struct
51 {
52 char *tag;
53 char type;
54 char cVal;
55 int iVal;
56 float fVal;
57 char *sVal;
58 } OPT_FIELDS;
59
60 typedef struct
61 {
62 char *QNAME;
63 short FLAG;
64 char *RNAME;
65 int POS;
66 unsigned char MAPQ;
67 char *CIGAR;
68 char *MRNAME;
69 int MPOS;
70 int ISIZE;
71 char *SEQ;
72 char *QUAL;
73
74 int optSize;
75 OPT_FIELDS *optFields;
76 } SAM;
77
78 int initOutput(char *fileName, int compressed);
79 void (*finalizeOutput)();
80 void (*output)(SAM map);
81 void outputSAM(FILE *fp, SAM map);
82
83 FILE * getOutputFILE();
84
85 #endif