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comparison mrsfast-2.3.0.2/MrsFAST.h @ 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 #ifndef __MRS_FAST__
38 #define __MRS_FAST__
39
40 #include "Reads.h"
41
42 #define MAP_CHUNKS 15
43
44 // Pair is used to pre-processing and making the read index table
45 typedef struct
46 {
47 int hv;
48 int seqInfo;
49 } Pair;
50
51 typedef struct
52 {
53 int hv;
54 unsigned int *seqInfo;
55 } ReadIndexTable;
56
57
58 typedef struct mn
59 {
60 int loc;
61 char dir;
62 char err;
63 float score;
64 char md[40];
65 char chr[10];
66 } FullMappingInfo;
67
68 typedef struct lc
69 {
70 int loc[MAP_CHUNKS];
71 struct lc *next;
72 } MappingLocations;
73
74 typedef struct inf
75 {
76 int size;
77 MappingLocations *next;
78 } MappingInfo;
79
80 typedef struct
81 {
82 FILE * fp;
83 char name[400];
84 } FILE_STRUCT;
85
86 extern long long verificationCnt;
87 extern long long mappingCnt;
88 extern long long mappedSeqCnt;
89 extern long long completedSeqCnt;
90
91 void initFAST( Read *seqList,
92 int seqListSize,
93 int *samplingLocs,
94 int samplingLocsSize,
95 char *fileName);
96
97 void finalizeFAST();
98
99 int mapSingleEndSeq();
100 int mapPaiedEndSeq();
101 void outputPairedEnd();
102 void outputPairedEndDiscPP();
103 #endif