c_cpp/salusFstReCoord/src1/input.c

   1 #include <stdio.h>  // fprintf
   2 #include <zlib-ng.h>
   3
   4 #include "kseq.h"
   5 KSEQ_INIT(gzFile, zng_gzread)
   6 #include "common.h"
   7
   8 void fqReader_init(void) {
   9         int rc;
  10         const char *pattern = "R[0-9]{3}(:)?C[0-9]{3}";
  11         if ((rc = regcomp(&Parameters.regex, pattern, REG_EXTENDED)) != 0) {
  12                 regerror(rc, &Parameters.regex, Parameters.buffer, PARAMETERS_BUFFER_SIZE);
  13                 printf("[x]=%d=regcomp(\"%s\") failed with '%s'.\n", rc, pattern, Parameters.buffer);
  14                 exit(EXIT_FAILURE);
  15         }
  16         Parameters.ksfp = zng_gzopen(Parameters.inFastqFilename, "r");
  17         if (unlikely(Parameters.ksfp == NULL)) {
  18                 fprintf(stderr, "[x]gzopen error on opening [%s]: %s.\n", Parameters.inFastqFilename, strerror(errno));
  19                 exit(1);
  20         }
  21         rc = zng_gzbuffer(Parameters.ksfp, GZBUFSIZE);
  22         if (unlikely(rc != 0)) {
  23                 fprintf(stderr, "[x]gzbuffer error: %s.\n", strerror(errno));
  24                 exit(1);
  25         }
  26         Parameters.kseq = kseq_init(Parameters.ksfp);
  27 }
  28
  29 void fqReader_destroy(void) {
  30         regfree(&Parameters.regex);
  31         kseq_destroy(Parameters.kseq);
  32         zng_gzclose(Parameters.ksfp);
  33 }
  34
  35 void fill_worker(int_least16_t worker_id) {
  36         kseq_t *seq = Parameters.kseq;
  37         workerArray_t *worker = &Parameters.workerArray[worker_id];
  38         uint64_t index = 0;
  39         regmatch_t matches[2];
  40
  41         for (uint64_t index = 0; index < JOBITEMSIZE; index++) {
  42                 fstBCdata_t *fstBCdata_p = &worker->input_array[index];
  43                 if (kseq_read(seq) >= MINBARCODELEN) {
  44                         // strncpy((char *)fstBCdata_p->name, seq->name.s, sizeof(fstBCdata_p->name));
  45                         STRcpyARRAY(fstBCdata_p->name, seq->name.s);
  46                         /* seq->comment.s is discarded */
  47                         STRcpyARRAY(fstBCdata_p->seq, seq->seq.s);
  48                         STRcpyARRAY(fstBCdata_p->qual, seq->qual.s);
  49                         if (unlikely(seq->comment.l > 0)) {
  50                                 if (likely(fstBCdata_p->comment != NULL)) {
  51                                         size_t oldSize = MALLOCSIZE(fstBCdata_p->comment);
  52                                         if (unlikely(1 + seq->comment.l > oldSize)) {
  53                                                 free(fstBCdata_p->comment);
  54                                                 fstBCdata_p->comment = strdup(seq->comment.s);
  55                                         } else {
  56                                                 STRcpySTR(fstBCdata_p->comment, seq->comment.s);
  57                                         }
  58                                 }
  59                         } else {
  60                                 if (unlikely(fstBCdata_p->comment != NULL)) {
  61                                         free(fstBCdata_p->comment);
  62                                         fstBCdata_p->comment = NULL;
  63                                 }
  64                         }
  65 #ifndef RELEASE
  66                         fprintf(stderr, "- %llu -\n", index);
  67                         ARRAYcpySTR(Parameters.buffer, fstBCdata_p->name);
  68                         // snprintf(Parameters.buffer, 1 + sizeof(fstBCdata_p->name), "%s", fstBCdata_p->name);
  69                         fprintf(stderr, "->Name:[%s]\n", Parameters.buffer);
  70                         ARRAYcpySTR(Parameters.buffer, fstBCdata_p->seq);
  71                         fprintf(stderr, "->Sequ:[%s]\n", Parameters.buffer);
  72                         ARRAYcpySTR(Parameters.buffer, fstBCdata_p->qual);
  73                         fprintf(stderr, "->Qual:[%s]\n", Parameters.buffer);
  74 #endif
  75                 } else {
  76                         fstBCdata_p->name[0] = '\0';
  77                         fstBCdata_p->seq[0] = '\0';
  78                         fstBCdata_p->qual[0] = '\0';
  79                 }
  80                 // continue;
  81         }
  82         // Update the worker's flag to indicate the processing is complete
  83         atomic_store(&worker->flag, 1);
  84 }