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comparison mrfast-2.1.0.5/RefGenome.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 <string.h>
46 #include <ctype.h>
47 #include "Common.h"
48 #include "RefGenome.h"
49
50 FILE *_rg_fp;
51 char *_rg_gen;
52 char *_rg_name;
53 int _rg_offset;
54 int _rg_contGen;
55
56 /**********************************************/
57 int initLoadingRefGenome(char *fileName)
58 {
59 char ch;
60 _rg_fp = fileOpen (fileName, "r");
61 if (fscanf(_rg_fp, "%c", &ch))
62 {
63 if (ch == '>')
64 {
65 _rg_contGen = 0;
66 _rg_offset = 0;
67 _rg_gen = getMem(CONTIG_MAX_SIZE);
68 _rg_name = getMem(CONTIG_NAME_SIZE);
69 return 1;
70 }
71 }
72 return 0;
73 }
74 /**********************************************/
75 void finalizeLoadingRefGenome()
76 {
77 freeMem(_rg_gen, CONTIG_MAX_SIZE);
78 freeMem(_rg_name, CONTIG_NAME_SIZE);
79 fclose(_rg_fp);
80 }
81 /**********************************************/
82 int loadRefGenome(char **refGen, char **refGenName, int *refGenOff)
83 {
84 char ch;
85 int i;
86 int returnVal = 0;
87 int actualSize=0;
88 int size;
89 char *tmp;
90
91 // New Conting
92 if (!_rg_contGen)
93 {
94 size = 0;
95 tmp = fgets(_rg_name, SEQ_MAX_LENGTH, _rg_fp);
96 }
97 else
98 {
99 size=strlen(_rg_gen);
100 for( i = 0 ; i < CONTIG_OVERLAP ; i++ )
101 {
102
103 _rg_gen[i] = _rg_gen[size-CONTIG_OVERLAP+i];
104 if (_rg_gen[i] != 'N')
105 actualSize++;
106 }
107 size = CONTIG_OVERLAP;
108 }
109 while( fscanf(_rg_fp, "%c", &ch) > 0 )
110 {
111 if (ch == '>')
112 {
113 _rg_contGen = 0;
114 returnVal = 1;
115 break;
116 }
117 else if (!isspace(ch))
118 {
119 ch = toupper(ch);
120 _rg_gen[size++] = ch;
121 if (ch != 'N')
122 {
123 actualSize++;
124 }
125 if (actualSize == CONTIG_SIZE || size == CONTIG_MAX_SIZE)
126 {
127 _rg_contGen = 1;
128 returnVal=1;
129 break;
130 }
131 }
132
133 }
134
135 _rg_gen[size] = '\0';
136 for (i=strlen(_rg_name)-1; i >= 0; i--)
137 if (!isspace(_rg_name[i]))
138 break;
139 _rg_name[i+1] = '\0';
140
141 *refGenOff = _rg_offset;
142 *refGenName = _rg_name;
143 *refGen = _rg_gen;
144
145 if (_rg_contGen == 1)
146 {
147 _rg_offset += size-CONTIG_OVERLAP;
148 }
149 else
150 {
151 _rg_offset = 0;
152 }
153
154
155 return returnVal;
156 }
157 /**********************************************/