Mercurial > repos > calkan > mrfast

comparison mrfast-2.1.0.5/MrFAST.h @ 1:d4054b05b015 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Version update to 2.1.0.5
author calkan
date Fri, 09 Mar 2012 07:35:51 -0500
parents
children
comparison
equal deleted inserted replaced
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 /*
33 Authors:
34 Farhad Hormozdiari
35 Faraz Hach
36 Can Alkan
37 Emails:
38 farhadh AT uw DOT edu
39 fhach AT cs DOT sfu DOT ca
40 calkan AT uw DOT edu
41 */
42
43
44
45 #ifndef __MR_FAST__
46 #define __MR_FAST__
47
48 #include "Reads.h"
49
50 #define MAP_CHUNKS 15
51 #define MAX_CIGAR_SIZE 100
52
53
54 // Pair is used to pre-processing and making the read index table
55 typedef struct
56 {
57 int hv;
58 //char hv[50];
59 int readNumber;
60 } Pair;
61
62 typedef struct
63 {
64 int hv;
65 unsigned int *seqInfo;
66 } ReadIndexTable;
67
68
69 typedef struct
70 {
71 int loc;
72 char dir;
73 int err;
74 float score;
75 char md[MAX_CIGAR_SIZE];
76 char chr[20];
77 char cigar[MAX_CIGAR_SIZE];
78 int cigarSize;
79 int mdSize;
80 } FullMappingInfo;
81
82 typedef struct
83 {
84 int loc;
85 char dir;
86 int err;
87 float score;
88 char md[MAX_CIGAR_SIZE];
89 char chr[20];
90 char cigar[MAX_CIGAR_SIZE];
91 int cigarSize;
92 int mdSize;
93 } BestFullMappingInfo;
94
95 typedef struct lc
96 {
97 char md[MAP_CHUNKS][MAX_CIGAR_SIZE];
98 int mdSize[MAP_CHUNKS];
99
100 char cigar[MAP_CHUNKS][MAX_CIGAR_SIZE];
101 int cigarSize[MAP_CHUNKS];
102
103 int err[MAP_CHUNKS];
104 int loc[MAP_CHUNKS];
105 struct lc *next;
106 } MappingLocations;
107
108 typedef struct inf
109 {
110 int size;
111 MappingLocations *next;
112 } MappingInfo;
113
114 typedef struct
115 {
116 FILE * fp;
117 char name[400];
118 } FILE_STRUCT;
119
120 typedef struct
121 {
122 FullMappingInfo *mi;
123 int size;
124 } FullMappingInfoLink;
125
126
127 typedef struct
128 {
129 char readString[200];
130 char ref[200];
131 int err;
132 char matrix[200];
133 } extraCaching;
134
135 extern long long verificationCnt;
136 extern long long mappingCnt;
137 extern long long mappedSeqCnt;
138 extern long long completedSeqCnt;
139
140 void initFAST( Read *seqList,
141 int seqListSize,
142 int *samplingLocs,
143 int samplingLocsSize,
144 char *fileName);
145
146 void initVerifiedLocs();
147 void initLookUpTable();
148 void initBestMapping();
149 void initBestConcordantDiscordant(int readNumber);
150
151 void finalizeFAST();
152 void finalizeBestSingleMapping();
153 void finalizeBestConcordantDiscordant();
154 void finalizeOEAReads(char *);
155
156
157 int mapAllSingleEndSeq();
158 void mapSingleEndSeq(unsigned int *l1, int s1, int readNumber, int readSegment, int direction);
159 void mapPairedEndSeqList(unsigned int *l1, int s1, int readNumber, int readSegment, int direction);
160
161 void mapPairedEndSeq();
162
163 void outputPairedEnd();
164 void outputPairedEndDiscPP();
165
166
167 void outputPairFullMappingInfo(FILE *fp, int readNumber);
168 void setPairFullMappingInfo(int readNumber, FullMappingInfo mi1, FullMappingInfo mi2);
169 void setFullMappingInfo(int readNumber, int loc, int dir, int err, int score, char *md, char * refName, char *cigar);
170
171 void outputAllTransChromosal();
172 void outputTransChromosal(char *fileName1, char *fileName2, FILE * fp_out);
173
174 void generateSNPSAM(char *matrix, int matrixLength, char *outputSNP);
175 void generateCigar(char *matrix, int matrixLength, char *cigar);
176 void generateCigarFromMD(char *mistmatch, int mismatchLength, char *cigar);
177
178 int msfHashVal(char *seq);
179
180 int backwardEditDistance2SSE2(char *a, int lena, char *b,int lenb);
181 int forwardEditDistance2SSE2(char *a, int lena, char *b,int lenb);
182
183 int forwardEditDistanceSSE2G(char *a, int lena, char *b,int lenb);
184 int backwardEditDistanceSSE2G(char *a, int lena, char *b,int lenb);
185
186 int forwardEditDistance4SSE2(char *a, int lena, char *b,int lenb);
187 int backwardEditDistance4SSE2(char *a, int lena, char *b,int lenb);
188
189 int forwardEditDistanceSSE2Extention(char *a, int lena, char *b,int lenb);
190 int backwardEditDistanceSSE2Extention(char *a, int lena, char *b,int lenb);
191
192
193 /***********************************/
194
195 int editDistance(int refIndex, char *seq, int seqLength, char *matrix);
196
197 int verifySingleEndEditDistance(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength,
198 char *matrix, int *map_location, short *seqHashValue);
199
200 int verifySingleEndEditDistance2(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength,
201 char *matrix, int *map_location, short *seqHashValue);
202
203 int verifySingleEndEditDistance4(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength,
204 char *matrix, int *map_location, short *seqHashValue);
205
206 int verifySingleEndEditDistanceExtention(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength,
207 char *matrix, int *map_location, short *seqHashValue);
208
209 #endif