|
1
|
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
|
