Mercurial > repos > calkan > mrcanavar

comparison mrcanavar-0.34/utils.c @ 0:86522a0b5f59 default tip

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Uploaded source code for mrCaNaVaR
author calkan
date Tue, 21 Feb 2012 10:44:13 -0500
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-1:000000000000 0:86522a0b5f59
1
2 #include "utils.h"
3
4
5
6 void print_error(char *msg){
7 fprintf(stderr, "\nmrCaNaVaR version %s.\nLast update: %s.\n", VERSION, LAST_UPDATE);
8 fprintf(stderr, "\n%s\n", msg);
9 fprintf(stderr, "Invoke parameter -h for help.\n");
10 exit (0);
11 }
12
13 void set_runmode(enum MODETYPE NEWMODE){
14 if (RUNMODE != NONE && RUNMODE != NEWMODE){
15 print_error("Select one run mode only.\n");
16 }
17 RUNMODE = NEWMODE;
18 }
19
20 void set_gender(enum GENDERTYPE SET){
21 if (GENDER != AUTODETECT && RUNMODE != SET){
22 print_error("Select only one of --xx or --xy.\n");
23 }
24 GENDER= SET;
25 }
26
27 void set_str(char **target, char *source){
28
29 if (*target != NULL) free((*target));
30
31 (*target) = (char *) malloc(sizeof(char) * (strlen(source)+1));
32
33 strncpy((*target), source, (strlen(source)+1));
34
35 }
36
37
38 void init_globals(void){
39 GENOME_FASTA = NULL;
40 GENOME_CONF = NULL;
41 GENOME_GAPS = NULL;
42 RUNMODE = NONE;
43 GENDER = AUTODETECT;
44 MULTGC = 0;
45 MAX_GC_CORR = 20.0;
46 MIN_GC_CORR = 0.05;
47 VERBOSE = 0;
48
49 num_chrom = 0;
50
51 CHECKSAM = 1;
52
53 /* set window size defaults */
54
55 LW_SIZE = 5000;
56 SW_SIZE = 1000;
57 CW_SIZE = 1000;
58 LW_SLIDE = 1000;
59 SW_SLIDE = 1000;
60
61 LW_MEAN = 0.0;
62 SW_MEAN = 0.0;
63 CW_MEAN = 0.0;
64
65 LW_STD = 0.0;
66 SW_STD = 0.0;
67 CW_STD = 0.0;
68
69 CONT_WINDOW = 7;
70 CUT_WINDOW = 6;
71
72 }
73
74
75 FILE *my_fopen(char *fname, char *mode, char GZ){
76 FILE *fp;
77
78
79 if (!GZ)
80 fp = fopen(fname, mode);
81 else
82 fp = gzopen(fname, mode);
83
84 if (fp == NULL){
85 fprintf(stderr, "Unable to open file %s in %s mode.", fname, mode[0]=='w' ? "write" : "read");
86 exit (0);
87 }
88
89 return fp;
90 }
91
92
93 void saveRefConfig(char *configFile){
94
95 int i;
96 int wcnt;
97 char chrom_name_len;
98 int retVal;
99 FILE *config;
100
101 config = my_fopen(configFile, "w", 0);
102
103 /* sort the chromosomes pointer array */
104
105 qsort(chromosomes, num_chrom, sizeof (struct chrom *), compChr);
106
107
108 /* start with the magicNum, I will use this as a format check when loading */
109 retVal = fwrite(&magicNum, sizeof(magicNum), 1, config);
110
111 /* window sizes / slides */
112
113 retVal = fwrite(&LW_SIZE, sizeof(LW_SIZE), 1, config);
114 retVal = fwrite(&SW_SIZE, sizeof(SW_SIZE), 1, config);
115 retVal = fwrite(&CW_SIZE, sizeof(CW_SIZE), 1, config);
116 retVal = fwrite(&LW_SLIDE, sizeof(LW_SLIDE), 1, config);
117 retVal = fwrite(&SW_SLIDE, sizeof(SW_SLIDE), 1, config);
118
119
120 /* reference genome numbers */
121
122 /* number of chromosomes */
123 retVal = fwrite(&num_chrom, sizeof(num_chrom), 1, config);
124
125 /* iterate through chromosomes, write their names, and window counts */
126
127 for (i=0; i<num_chrom; i++){
128 chrom_name_len = (char) strlen(chromosomes[i]->name);
129 retVal = fwrite(&chrom_name_len, sizeof(chrom_name_len), 1, config);
130 retVal = fwrite(chromosomes[i]->name, chrom_name_len * sizeof(char), 1, config);
131
132 retVal = fwrite(&(chromosomes[i]->length), sizeof(chromosomes[i]->length), 1, config);
133 retVal = fwrite(&(chromosomes[i]->lw_cnt), sizeof(chromosomes[i]->lw_cnt), 1, config);
134 retVal = fwrite(&(chromosomes[i]->sw_cnt), sizeof(chromosomes[i]->sw_cnt), 1, config);
135 retVal = fwrite(&(chromosomes[i]->cw_cnt), sizeof(chromosomes[i]->cw_cnt), 1, config);
136
137 /* long windows */
138 for (wcnt=0; wcnt<chromosomes[i]->lw_cnt; wcnt++){
139 retVal = fwrite(&(chromosomes[i]->lw[wcnt].start), sizeof(chromosomes[i]->lw[wcnt].start), 1, config);
140 retVal = fwrite(&(chromosomes[i]->lw[wcnt].end), sizeof(chromosomes[i]->lw[wcnt].end), 1, config);
141 retVal = fwrite(&(chromosomes[i]->lw[wcnt].gc), sizeof(chromosomes[i]->lw[wcnt].gc), 1, config);
142 }
143
144 /* short windows */
145 for (wcnt=0; wcnt<chromosomes[i]->sw_cnt; wcnt++){
146 retVal = fwrite(&(chromosomes[i]->sw[wcnt].start), sizeof(chromosomes[i]->sw[wcnt].start), 1, config);
147 retVal = fwrite(&(chromosomes[i]->sw[wcnt].end), sizeof(chromosomes[i]->sw[wcnt].end), 1, config);
148 retVal = fwrite(&(chromosomes[i]->sw[wcnt].gc), sizeof(chromosomes[i]->sw[wcnt].gc), 1, config);
149 }
150
151 /* copy windows */
152 for (wcnt=0; wcnt<chromosomes[i]->cw_cnt; wcnt++){
153 retVal = fwrite(&(chromosomes[i]->cw[wcnt].start), sizeof(chromosomes[i]->cw[wcnt].start), 1, config);
154 retVal = fwrite(&(chromosomes[i]->cw[wcnt].end), sizeof(chromosomes[i]->cw[wcnt].end), 1, config);
155 retVal = fwrite(&(chromosomes[i]->cw[wcnt].gc), sizeof(chromosomes[i]->cw[wcnt].gc), 1, config);
156 }
157
158 }
159
160 fclose(config);
161
162 }
163
164
165
166
167 void loadRefConfig(char *configFile){
168
169 int i;
170 int wcnt;
171 char chrom_name_len;
172 char readString[MAX_STR];
173 int retVal;
174
175 int isMagicNum;
176
177 FILE *config;
178
179 config = my_fopen(configFile, "r", 0);
180
181 /* start with the magicNum, use this as a format check when loading */
182 retVal = fread(&isMagicNum, sizeof(isMagicNum), 1, config);
183
184 if (isMagicNum != magicNum)
185 print_error("Reference configuration file seems to be invalid or corrupt.\n");
186
187
188 fprintf(stdout, "Loading reference configuration, hold on ... ");
189 fflush(stdout);
190
191 /* window sizes / slides */
192
193 retVal = fread(&LW_SIZE, sizeof(LW_SIZE), 1, config);
194 retVal = fread(&SW_SIZE, sizeof(SW_SIZE), 1, config);
195 retVal = fread(&CW_SIZE, sizeof(CW_SIZE), 1, config);
196 retVal = fread(&LW_SLIDE, sizeof(LW_SLIDE), 1, config);
197 retVal = fread(&SW_SLIDE, sizeof(SW_SLIDE), 1, config);
198
199
200 /* reference genome numbers */
201
202 /* number of chromosomes */
203 retVal = fread(&num_chrom, sizeof(num_chrom), 1, config);
204
205 /* create chromosomes data structure */
206
207 chromosomes = (struct chrom **) malloc(sizeof(struct chrom *) * num_chrom);
208 for (i=0; i<num_chrom; i++)
209 chromosomes[i] = (struct chrom *) malloc(sizeof(struct chrom) * num_chrom);
210
211 /* iterate through chromosomes, write their names, and window counts */
212
213 for (i=0; i<num_chrom; i++){
214
215 retVal = fread(&chrom_name_len, sizeof(chrom_name_len), 1, config);
216
217 retVal = fread(readString, chrom_name_len * sizeof(char), 1, config);
218 readString[chrom_name_len] = 0;
219 trimspace(readString);
220
221 set_str(&(chromosomes[i]->name), readString);
222
223 retVal = fread(&(chromosomes[i]->length), sizeof(chromosomes[i]->length), 1, config);
224 retVal = fread(&(chromosomes[i]->lw_cnt), sizeof(chromosomes[i]->lw_cnt), 1, config);
225 retVal = fread(&(chromosomes[i]->sw_cnt), sizeof(chromosomes[i]->sw_cnt), 1, config);
226 retVal = fread(&(chromosomes[i]->cw_cnt), sizeof(chromosomes[i]->cw_cnt), 1, config);
227
228 /* create windows structures */
229
230
231 chromosomes[i]->lw = (struct window *) malloc (sizeof(struct window) * chromosomes[i]->lw_cnt);
232 chromosomes[i]->sw = (struct window *) malloc (sizeof(struct window) * chromosomes[i]->sw_cnt);
233 chromosomes[i]->cw = (struct window *) malloc (sizeof(struct window) * chromosomes[i]->cw_cnt);
234
235
236
237 /* long windows */
238 for (wcnt=0; wcnt<chromosomes[i]->lw_cnt; wcnt++){
239 retVal = fread(&(chromosomes[i]->lw[wcnt].start), sizeof(chromosomes[i]->lw[wcnt].start), 1, config);
240 retVal = fread(&(chromosomes[i]->lw[wcnt].end), sizeof(chromosomes[i]->lw[wcnt].end), 1, config);
241 retVal = fread(&(chromosomes[i]->lw[wcnt].gc), sizeof(chromosomes[i]->lw[wcnt].gc), 1, config);
242 // this is the default, auto-control-picker will fix this
243 chromosomes[i]->lw[wcnt].isControl = 1;
244 chromosomes[i]->lw[wcnt].depth = 0.0;
245 }
246
247 /* short windows */
248 for (wcnt=0; wcnt<chromosomes[i]->sw_cnt; wcnt++){
249 retVal = fread(&(chromosomes[i]->sw[wcnt].start), sizeof(chromosomes[i]->sw[wcnt].start), 1, config);
250 retVal = fread(&(chromosomes[i]->sw[wcnt].end), sizeof(chromosomes[i]->sw[wcnt].end), 1, config);
251 retVal = fread(&(chromosomes[i]->sw[wcnt].gc), sizeof(chromosomes[i]->sw[wcnt].gc), 1, config);
252 chromosomes[i]->sw[wcnt].isControl = 1;
253 chromosomes[i]->sw[wcnt].depth = 0.0;
254 }
255
256 /* copy windows */
257 for (wcnt=0; wcnt<chromosomes[i]->cw_cnt; wcnt++){
258 retVal = fread(&(chromosomes[i]->cw[wcnt].start), sizeof(chromosomes[i]->cw[wcnt].start), 1, config);
259 retVal = fread(&(chromosomes[i]->cw[wcnt].end), sizeof(chromosomes[i]->cw[wcnt].end), 1, config);
260 retVal = fread(&(chromosomes[i]->cw[wcnt].gc), sizeof(chromosomes[i]->cw[wcnt].gc), 1, config);
261 chromosomes[i]->cw[wcnt].isControl = 1;
262 chromosomes[i]->cw[wcnt].depth = 0.0;
263 }
264
265 /* fill in the rest of the chromosomes structure */
266
267 }
268
269 fprintf(stdout, "[OK]. %d chromosomes loaded.\n", num_chrom);
270
271 fclose(config);
272 }
273
274
275
276 static int compChr(const void *p1, const void *p2){
277 /* compare function to sort the chromosome pointer array */
278 struct chrom *a, *b;
279
280 a = *((struct chrom **)p1);
281 b = *((struct chrom **)p2);
282
283
284 return (strcmp ( a->name, b->name) );
285
286 }
287
288
289 int endswith(char *src, char *end){
290
291
292 int endlen = strlen(end);
293 int srclen = strlen(src);
294 int copyindex;
295
296
297 if (endlen > srclen)
298 return 0;
299
300 copyindex = srclen - endlen;
301
302 if (memcmp(src+copyindex, end, endlen))
303 return 0;
304 else
305 return 1;
306
307
308 }
309
310 void trimspace(char *str){
311 int len;
312 len = strlen(str) - 1;
313 while(1){
314 if (isspace(str[len]))
315 str[len--]=0;
316 else
317 break;
318 }
319 }