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date Wed, 12 Dec 2018 07:18:40 -0500
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1 /*********
2
3 File CHROMEISTER.c
4 Author EPW <estebanpw@uma.es>
5 Description Computes hits and generates a dotplot
6
7 USAGE Usage is described by calling ./CHROMEISTER --help
8
9
10
11 **********/
12
13
14 #include <stdio.h>
15 #include <stdlib.h>
16 #include <math.h>
17 #include <string.h>
18 #include <ctype.h>
19 #include "structs.h"
20 #include "alignmentFunctions.h"
21 #include "commonFunctions.h"
22 #define STARTING_SEQS 1000
23 #define PIECE_OF_DB_REALLOC 3200000 //half a gigabyte if divided by 8 bytes
24 #define RANGE 2
25
26 uint64_t custom_kmer = 32; // Defined as external in structs.h
27 uint64_t diffuse_z = 4; // Defined as external in structs.h
28
29 uint64_t get_seq_len(FILE * f);
30
31
32 void init_args(int argc, char ** av, FILE ** query, FILE ** database, FILE ** out_database, uint64_t * custom_kmer, uint64_t * dimension, uint64_t * diffuse_z);
33
34 int main(int argc, char ** av){
35
36
37 /*
38 //Store positions of kmers
39 uint64_t n_pools_used = 0;
40 //Mempool_l * mp = (Mempool_l *) malloc(MAX_MEM_POOLS*sizeof(Mempool_l));
41 //if(mp == NULL) terror("Could not allocate vectors for memory pools");
42 Mempool_l mp[MAX_MEM_POOLS];
43 init_mem_pool_llpos(&mp[n_pools_used]);
44 //llpos * aux;
45
46 uint64_t n_pools_used_AVL = 0;
47 Mempool_AVL mp_AVL[MAX_MEM_POOLS];
48 init_mem_pool_AVL(&mp_AVL[n_pools_used_AVL]);
49 */
50 Tuple_hits * thit;
51
52 /*
53 AVLTree * root = NULL;
54 root = insert_AVLTree(root, 10, mp_AVL, &n_pools_used_AVL, 0, mp, &n_pools_used);
55
56 llpos * some = find_AVLTree(root, 25);
57 while(some != NULL){
58 printf("#%"PRIu64", ", some->pos); some = some->next;
59 }
60 */
61
62 uint64_t i, j;
63
64 //query to read kmers from, database to find seeds
65 FILE * query = NULL, * database = NULL, * out_database = NULL;
66 uint64_t dimension = 1000; // Default 1000 * 1000
67
68
69 init_args(argc, av, &query, &database, &out_database, &custom_kmer, &dimension, &diffuse_z);
70
71
72
73 unsigned char char_converter[91];
74 char_converter[(unsigned char)'A'] = 0;
75 char_converter[(unsigned char)'C'] = 1;
76 char_converter[(unsigned char)'G'] = 2;
77 char_converter[(unsigned char)'T'] = 3;
78
79
80 // Variables to account for positions
81 // Print info
82 fprintf(stdout, "[INFO] Loading database\n");
83 // Variables to read kmers
84 char c = 'N'; //Char to read character
85 // Current length of array and variables for the buffer
86 uint64_t idx = 0, r = 0;
87
88 //Vector to read in batches
89 char * temp_seq_buffer = NULL;
90 if ((temp_seq_buffer = calloc(READBUF, sizeof(char))) == NULL) {
91 terror("Could not allocate memory for read buffer");
92 }
93
94 //Dimensional matrix
95 uint64_t ** representation = (uint64_t **) calloc(dimension+1, sizeof(uint64_t *));
96 if(representation == NULL) terror("Could not allocate representation");
97 for(i=0; i<dimension+1; i++){
98 representation[i] = (uint64_t *) calloc(dimension+1, sizeof(uint64_t));
99 if(representation[i] == NULL) terror("Could not allocate second loop representation");
100 }
101
102 /*
103 fseek(database, 0, SEEK_END);
104 uint64_t aprox_len_query = ftell(database);
105 uint64_t aprox_len_db = aprox_len_query;
106 rewind(database);
107 */
108 uint64_t aprox_len_query = get_seq_len(database);
109 uint64_t aprox_len_db = aprox_len_query;
110
111 uint64_t a_hundreth = (aprox_len_query/100);
112
113 unsigned char curr_kmer[custom_kmer], reverse_kmer[custom_kmer];
114 curr_kmer[0] = reverse_kmer[0] = '\0';
115 uint64_t word_size = 0, word_size_rev = 0;
116
117 //To hold all information related to database
118 uint64_t current_len = 0;
119
120 //To force reading from the buffer
121 idx = READBUF + 1;
122
123 //unsigned char aux_kmer[custom_kmer+1];
124
125 //Vector to store query seq
126 unsigned char * seq_vector_query = (unsigned char *) malloc(READBUF*sizeof(unsigned char));
127 if(seq_vector_query == NULL) terror("Could not allocate memory for query vector");
128
129 /*
130 Container * ct = (Container *) calloc(1, sizeof(Container));
131 if(ct == NULL) terror("Could not allocate container");
132 */
133
134
135
136 Index * ctidx = (Index *) calloc(1, sizeof(Index));
137 if(ctidx == NULL) terror("Could not allocate container");
138
139
140 //begin = clock();
141
142
143 c = buffered_fgetc(temp_seq_buffer, &idx, &r, database);
144 while((!feof(database) || (feof(database) && idx < r))){
145
146 if(c == '>'){
147
148
149
150 while(c != '\n') c = buffered_fgetc(temp_seq_buffer, &idx, &r, database); //Skip ID
151
152
153 while(c != '>' && (!feof(database) || (feof(database) && idx < r))){ //Until next id
154 c = buffered_fgetc(temp_seq_buffer, &idx, &r, database);
155 c = toupper(c);
156 if(c == 'A' || c == 'C' || c == 'G' || c == 'T'){
157 curr_kmer[word_size] = (unsigned char) c;
158 if(word_size < custom_kmer) ++word_size;
159 ++current_len;
160 if(current_len % a_hundreth == 0){
161 fprintf(stdout, "\r%"PRIu64"%%...", 1+100*current_len/aprox_len_query);
162 //printf("%"PRIu64"%%..wasted: (%e) (%e)", 1+100*pos_in_query/aprox_len_query, (double)(wasted_cycles_forward)/CLOCKS_PER_SEC, (double)(wasted_cycles_reverse)/CLOCKS_PER_SEC);
163 fflush(stdout);
164 }
165
166
167
168 }else{ //It can be anything (including N, Y, X ...)
169
170 if(c != '\n' && c != '>'){
171 word_size = 0;
172 // data_database.sequences[pos_in_database++] = (unsigned char) 'N'; //Convert to N
173 ++current_len;
174
175 }
176 }
177 //if(current_len % 1000000 == 0) printf(" curr len %" PRIu64"\n", current_len);
178 if(word_size == custom_kmer){
179 //write to hash table
180
181
182 thit = &ctidx->table[char_converter[curr_kmer[0]]][char_converter[curr_kmer[1]]][char_converter[curr_kmer[2]]]
183 [char_converter[curr_kmer[3]]][char_converter[curr_kmer[4]]][char_converter[curr_kmer[5]]]
184 [char_converter[curr_kmer[6]]][char_converter[curr_kmer[7]]][char_converter[curr_kmer[8]]]
185 [char_converter[curr_kmer[9]]][char_converter[curr_kmer[10]]][char_converter[curr_kmer[11]]];
186
187 /*
188 typedef struct tuple_hits{
189 int repetition;
190 int hit_count;
191 uint64_t key;
192 uint64_t pos;
193 } Tuple_hits;
194 */
195
196 if(thit->repetition == FALSE){
197 // Then we can insert
198 thit->hit_count = 0;
199 thit->key = collisioned_hash(&curr_kmer[0], custom_kmer);
200 thit->pos = current_len;
201 }else{
202 // Otherwise we break it
203 thit->repetition = TRUE;
204 }
205
206 //thit->root = insert_AVLTree(thit->root, hashOfWord(&curr_kmer[0], custom_kmer, FIXED_K), mp_AVL, &n_pools_used_AVL, current_len, mp, &n_pools_used);
207 //thit->root = insert_AVLTree(thit->root, collisioned_hash(&curr_kmer[0], custom_kmer), mp_AVL, &n_pools_used_AVL, current_len, mp, &n_pools_used);
208
209
210
211 // Non overlapping
212 word_size = 0;
213
214
215 // Overlapping
216 //memmove(&curr_kmer[0], &curr_kmer[1], custom_kmer-1);
217 //--word_size;
218 }
219 }
220 word_size = 0;
221
222 }else{
223 c = buffered_fgetc(temp_seq_buffer, &idx, &r, database);
224 }
225
226 }
227
228
229 //end = clock();
230
231 // data_database.total_len = pos_in_database;
232
233 //fprintf(stdout, "[INFO] Database loaded and of length %"PRIu64". Hash table building took %e seconds\n", data_database.total_len, (double)(end-begin)/CLOCKS_PER_SEC);
234 fprintf(stdout, "[INFO] Database loaded and of length %"PRIu64".\n", current_len);
235 //close database
236 fclose(database);
237
238
239
240 //begin = clock();
241
242
243
244
245
246 double pixel_size_db = (double) dimension / (double) current_len;
247 double ratio_db = (double) current_len / dimension;
248
249
250 // Get file length
251
252 //fseek(query, 0, SEEK_END);
253 //aprox_len_query = ftell(query);
254 //rewind(query);
255 aprox_len_query = get_seq_len(query);
256
257 //uint64_t reallocs_hash_holder_table = 1;
258 //uint64_t n_items_hash_holder_table = aprox_len_query / 5;
259
260 //Hash_holder * hash_holder_table = (Hash_holder *) calloc(n_items_hash_holder_table, sizeof(Hash_holder));
261 //if(hash_holder_table == NULL) terror("Could not allocate hash holding table");
262
263 a_hundreth = (aprox_len_query/100);
264 double pixel_size_query = (double) dimension / (double) aprox_len_query;
265 double ratio_query = (double) aprox_len_query / dimension;
266
267
268 double i_r_fix = MAX(1.0, custom_kmer * pixel_size_query);
269 double j_r_fix = MAX(1.0, custom_kmer * pixel_size_db);
270
271
272
273 fprintf(stdout, "[INFO] Ratios: Q [%e] D [%e]. Lenghts: Q [%"PRIu64"] D [%"PRIu64"]\n", ratio_query, ratio_db, aprox_len_query, current_len);
274 fprintf(stdout, "[INFO] Pixel size: Q [%e] D [%e].\n", pixel_size_query, pixel_size_db);
275
276
277 fprintf(stdout, "[INFO] Computing absolute hit numbers.\n");
278
279
280 current_len = 0;
281
282 //llpos * the_original_hit;
283
284 //To force reading from the buffer
285 idx = READBUF + 1;
286 c = buffered_fgetc(temp_seq_buffer, &idx, &r, query);
287 //uint64_t c_hash_holder = 0;
288
289 while((!feof(query) || (feof(query) && idx < r))){
290
291 if(c == '>'){
292 word_size = 0;
293 word_size_rev = custom_kmer-1;
294
295
296
297
298 while(c != '\n'){ c = buffered_fgetc(temp_seq_buffer, &idx, &r, query); } //Skip ID
299
300
301 while(c != '>' && (!feof(query) || (feof(query) && idx < r))){ //Until next id
302 c = buffered_fgetc(temp_seq_buffer, &idx, &r, query);
303 c = toupper(c);
304 if(c == 'A' || c == 'C' || c == 'G' || c == 'T'){
305
306 ++current_len;
307 if(current_len % a_hundreth == 0){
308 fprintf(stdout, "\r%"PRIu64"%%...", 1+100*current_len/aprox_len_query);
309 fflush(stdout);
310 }
311 curr_kmer[word_size] = (unsigned char) c;
312 ++word_size;
313
314 switch(c){
315 case ('A'): reverse_kmer[word_size_rev] = (unsigned)'T';
316 break;
317 case ('C'): reverse_kmer[word_size_rev] = (unsigned)'G';
318 break;
319 case ('G'): reverse_kmer[word_size_rev] = (unsigned)'C';
320 break;
321 case ('T'): reverse_kmer[word_size_rev] = (unsigned)'A';
322 break;
323 }
324 if(word_size_rev != 0) --word_size_rev;
325
326
327
328
329 if(word_size == custom_kmer){
330
331
332 //hash_forward = hashOfWord(&curr_kmer[0], custom_kmer, FIXED_K);
333 //hash_reverse = hashOfWord(&reverse_kmer[0], custom_kmer, FIXED_K);
334 uint64_t hash_forward, hash_reverse;
335 hash_forward = collisioned_hash(&curr_kmer[0], custom_kmer);
336 hash_reverse = collisioned_hash(&reverse_kmer[0], custom_kmer);
337
338
339 thit = &ctidx->table[char_converter[curr_kmer[0]]][char_converter[curr_kmer[1]]][char_converter[curr_kmer[2]]]
340 [char_converter[curr_kmer[3]]][char_converter[curr_kmer[4]]][char_converter[curr_kmer[5]]]
341 [char_converter[curr_kmer[6]]][char_converter[curr_kmer[7]]][char_converter[curr_kmer[8]]]
342 [char_converter[curr_kmer[9]]][char_converter[curr_kmer[10]]][char_converter[curr_kmer[11]]];
343
344 //AVLTree * search = find_AVLTree(thit->root, hash_forward);
345
346 if(thit->repetition == FALSE && hash_forward == thit->key){
347 // Attention ::::: you were not removing the ones with count==1 earlier
348 thit->pos_in_y = current_len;
349 thit->hit_count++;
350 }
351
352 thit = &ctidx->table[char_converter[reverse_kmer[0]]][char_converter[reverse_kmer[1]]][char_converter[reverse_kmer[2]]]
353 [char_converter[reverse_kmer[3]]][char_converter[reverse_kmer[4]]][char_converter[reverse_kmer[5]]]
354 [char_converter[reverse_kmer[6]]][char_converter[reverse_kmer[7]]][char_converter[reverse_kmer[8]]]
355 [char_converter[reverse_kmer[9]]][char_converter[reverse_kmer[10]]][char_converter[reverse_kmer[11]]];
356
357 if(thit->repetition == FALSE && hash_reverse == thit->key){
358 // Attention ::::: you were not removing the ones with count==1 earlier
359 thit->pos_in_y = current_len;
360 thit->hit_count++;
361 }
362
363 /*
364 if(search != NULL && search->count == 1){ //If count is two, then it is a rep
365 thit->hit_count += search->count;
366
367 hash_holder_table[c_hash_holder].pos = current_len;
368 hash_holder_table[c_hash_holder].node = search;
369 hash_holder_table[c_hash_holder].th = thit;
370 ++c_hash_holder;
371 if(c_hash_holder == n_items_hash_holder_table*reallocs_hash_holder_table){
372 ++reallocs_hash_holder_table;
373 hash_holder_table = (Hash_holder *) realloc(hash_holder_table, n_items_hash_holder_table*reallocs_hash_holder_table*sizeof(Hash_holder));
374 if(hash_holder_table == NULL) terror("Could not realloc hash holder table");
375 }
376 }
377 */
378
379
380
381
382
383 //search = find_AVLTree(thit->root, hash_reverse);
384 /*
385 if(search != NULL && search->count == 1){ //If count is two, then it is a rep
386
387 thit->hit_count += search->count;
388 hash_holder_table[c_hash_holder].pos = current_len;
389 hash_holder_table[c_hash_holder].node = search;
390 hash_holder_table[c_hash_holder].th = thit;
391 ++c_hash_holder;
392 if(c_hash_holder == n_items_hash_holder_table*reallocs_hash_holder_table){
393 ++reallocs_hash_holder_table;
394 hash_holder_table = (Hash_holder *) realloc(hash_holder_table, n_items_hash_holder_table*reallocs_hash_holder_table*sizeof(Hash_holder));
395 if(hash_holder_table == NULL) terror("Could not realloc hash holder table");
396 }
397 }
398 */
399
400 // Overlapping
401
402 memmove(&curr_kmer[0], &curr_kmer[1], custom_kmer-1);
403 memmove(&reverse_kmer[1], &reverse_kmer[0], custom_kmer-1);
404 --word_size;
405
406 // Non overlapping
407 //word_size = 0;
408 //word_size_rev = custom_kmer-1;
409 }
410 }else{
411 if(c != '\n' && c != '>'){
412 word_size = 0;
413 word_size_rev = custom_kmer-1;
414 ++current_len;
415 }
416 }
417 }
418 }else{
419 c = buffered_fgetc(temp_seq_buffer, &idx, &r, query);
420 }
421
422 }
423
424 /// Out
425
426 fprintf(stdout, "Scanning hits table.\n");
427
428 a_hundreth = MAX(1, TOTAL_ENTRIES/100);
429 uint64_t t_computed = 0;
430 uint64_t w0,w1,w2,w3,w4,w5,w6,w7,w8,w9,w10,w11;
431 for(w0=0;w0<4;w0++){
432 for(w1=0;w1<4;w1++){
433 for(w2=0;w2<4;w2++){
434 for(w3=0;w3<4;w3++){
435 for(w4=0;w4<4;w4++){
436 for(w5=0;w5<4;w5++){
437 for(w6=0;w6<4;w6++){
438 for(w7=0;w7<4;w7++){
439 for(w8=0;w8<4;w8++){
440 for(w9=0;w9<4;w9++){
441 for(w10=0;w10<4;w10++){
442 for(w11=0;w11<4;w11++){
443
444 if(t_computed % a_hundreth == 0){
445 fprintf(stdout, "\r%"PRIu64"%%...", 1+100*t_computed/TOTAL_ENTRIES);
446 fflush(stdout);
447 }
448 ++t_computed;
449 Tuple_hits * taux = &ctidx->table[w0][w1][w2][w3][w4][w5][w6][w7][w8][w9][w10][w11];
450 if(taux->hit_count == 1){
451 // We plot it
452 // Convert scale to representation
453 uint64_t redir_db = (uint64_t) (taux->pos / (ratio_db));
454 uint64_t redir_query = (uint64_t) (taux->pos_in_y / (ratio_query));
455 double i_r = i_r_fix; double j_r = j_r_fix;
456 while((uint64_t) i_r >= 1 && (uint64_t) j_r >= 1){
457 if((int64_t) redir_query - (int64_t) i_r > 0 && (int64_t) redir_db - (int64_t) j_r > 0){
458 representation[(int64_t) redir_query - (int64_t) i_r][(int64_t) redir_db - (int64_t) j_r]++;
459 }else{
460 representation[redir_query][redir_db]++;
461 break;
462 }
463 i_r -= MIN(1.0, pixel_size_query);
464 j_r -= MIN(1.0, pixel_size_db);
465 }
466 }
467 }
468 }
469 }
470 }
471 }
472 }
473 }
474 }
475 }
476 }
477 }
478 }
479
480
481 //double average_hit = ((double) total_hits / (double) table_size);
482 //average_hit = 2.2;
483
484 /*
485 //fprintf(stdout, "[INFO] Total hit count is %"PRIu64" on a size of %"PRIu64" Avg = %e.\n", total_hits, table_size, average_hit);
486 fprintf(stdout, "[INFO] Total hit count is %"PRIu64" on a size of %"PRIu64" E' = %e.\n", total_hits, table_size, Eprime);
487
488
489
490
491
492 a_hundreth = MAX(1,c_hash_holder/100);
493
494 for(current_len = 0; current_len < c_hash_holder; current_len++){
495
496 if(current_len % a_hundreth == 0){
497 fprintf(stdout, "\r%"PRIu64"%%...", 1+100*current_len/c_hash_holder);
498 fflush(stdout);
499 }
500
501 aux = hash_holder_table[current_len].node->next;
502
503 //if(hash_holder_table[current_len].th->hit_count < (uint64_t) average_hit){
504 if(hash_holder_table[current_len].th->hit_count < (uint64_t) Eprime){
505 while(aux != NULL){
506 // Convert scale to representation
507 uint64_t redir_db = (uint64_t) (aux->pos / (ratio_db));
508 uint64_t redir_query = (uint64_t) (hash_holder_table[current_len].pos / (ratio_query));
509 double i_r = i_r_fix; double j_r = j_r_fix;
510 while((uint64_t) i_r >= 1 && (uint64_t) j_r >= 1){
511 if((int64_t) redir_query - (int64_t) i_r > 0 && (int64_t) redir_db - (int64_t) j_r > 0){
512 representation[(int64_t) redir_query - (int64_t) i_r][(int64_t) redir_db - (int64_t) j_r]++;
513 }else{
514 representation[redir_query][redir_db]++;
515 break;
516 }
517 i_r -= MIN(1.0, pixel_size_query);
518 j_r -= MIN(1.0, pixel_size_db);
519 }
520 aux = aux->next;
521 }
522 }
523 }
524 */
525
526
527 //end = clock();
528
529
530
531
532 //fprintf(stdout, "\n[INFO] Query length %"PRIu64". Hits completed. Took %e seconds\n", data_query.total_len, (double)(end-begin)/CLOCKS_PER_SEC);
533 fprintf(stdout, "\n[INFO] Query length %"PRIu64".\n", current_len);
534
535 //begin = clock();
536
537 //reads_per_thread = (uint64_t) (floorl((long double) data_query.n_seqs / (long double) n_threads));
538
539 fprintf(stdout, "[INFO] Writing matrix.\n");
540
541
542 uint64_t unique_diffuse = 0;
543 fprintf(out_database, "%"PRIu64"\n", aprox_len_query);
544 fprintf(out_database, "%"PRIu64"\n", aprox_len_db);
545 // And replace 2's with 1's
546
547 for(i=0; i<dimension+1; i++){
548 for(j=0; j<dimension; j++){
549 fprintf(out_database, "%"PRIu64" ", representation[i][j]);
550 unique_diffuse += representation[i][j];
551 }
552 fprintf(out_database, "%"PRIu64"\n", representation[i][dimension]);
553 unique_diffuse += representation[i][dimension];
554 }
555
556 fprintf(stdout, "[INFO] Found %"PRIu64" unique hits for z = %"PRIu64".\n", unique_diffuse, diffuse_z);
557
558
559
560 //free(ct->table);
561 //free(hash_holder_table);
562 /*
563 for(i=0;i<=n_pools_used_AVL;i++){
564 free(mp_AVL[i].base);
565 }
566
567 for(i=0;i<=n_pools_used;i++){
568 free(mp[i].base);
569 }
570 */
571 for(i=0;i<dimension;i++){
572 free(representation[i]);
573 }
574 free(representation);
575 if(out_database != NULL) fclose(out_database);
576
577 return 0;
578 }
579
580 void init_args(int argc, char ** av, FILE ** query, FILE ** database, FILE ** out_database, uint64_t * custom_kmer, uint64_t * dimension, uint64_t * diffuse_z){
581
582 int pNum = 0;
583 while(pNum < argc){
584 if(strcmp(av[pNum], "--help") == 0){
585 fprintf(stdout, "USAGE:\n");
586 fprintf(stdout, " CHROMEISTER -query [query] -db [database] -out [outfile]\n");
587 fprintf(stdout, "OPTIONAL:\n");
588 fprintf(stdout, " -kmer [Integer: k>1 (default 32)]\n");
589 fprintf(stdout, " -diffuse [Integer: z>0 (default 4)]\n");
590 fprintf(stdout, " -dimension Size of the output [Integer: d>0 (default 1000)]\n");
591 fprintf(stdout, " -out [File path]\n");
592 fprintf(stdout, " --help Shows help for program usage\n");
593 fprintf(stdout, "\n");
594 fprintf(stdout, "PLEASE NOTICE: The reverse complementary is calculated for the QUERY.\n");
595 exit(1);
596 }
597 if(strcmp(av[pNum], "-query") == 0){
598 *query = fopen64(av[pNum+1], "rt");
599 if(query==NULL) terror("Could not open query file");
600 }
601 if(strcmp(av[pNum], "-db") == 0){
602 *database = fopen64(av[pNum+1], "rt");
603 if(database==NULL) terror("Could not open database file");
604 }
605 if(strcmp(av[pNum], "-out") == 0){
606 *out_database = fopen(av[pNum+1], "wt");
607 if(out_database==NULL) terror("Could not open output database file");
608 }
609 if(strcmp(av[pNum], "-kmer") == 0){
610 *custom_kmer = (uint64_t) atoi(av[pNum+1]);
611 if(*custom_kmer < BYTES_IN_MER) terror("K-mer size must be larger than 4");
612 if(*custom_kmer % BYTES_IN_MER != 0) terror("K-mer size must be a multiple of 4");
613
614 }
615 if(strcmp(av[pNum], "-diffuse") == 0){
616 *diffuse_z = (uint64_t) atoi(av[pNum+1]);
617 if(*diffuse_z == 0 || *diffuse_z > 32) terror("Z must satisfy 0<z<=32");
618
619 }
620
621 if(strcmp(av[pNum], "-dimension") == 0){
622 *dimension = (uint64_t) atoi(av[pNum+1]);
623 if(*dimension < 1) terror("Dimension must be a positive integer");
624 }
625
626 pNum++;
627 }
628
629 if(*query==NULL || *database==NULL || *out_database==NULL) terror("A query, database and output file is required");
630 }
631
632 uint64_t get_seq_len(FILE * f) {
633 char c = '\0';
634 uint64_t l = 0;
635
636 while(!feof(f)){
637 c = getc(f);
638
639 if(c == '>'){
640 while(c != '\n') c = getc(f);
641 }
642 c = toupper(c);
643 if(c >= 'A' && c <= 'Z'){
644 ++l;
645 }
646 }
647
648
649 rewind(f);
650 return l;
651 }