sfs.cpp

#include "sfs.h"

sfs_t *init_sfs() {
  sfs_t *s = (sfs_t *)malloc(sizeof(sfs_t));
  s->rname = (char *)malloc(128 * sizeof(char));
  s->seq = NULL;
  return s;
}

void destroy_sfs(sfs_t *s) {
  free(s->rname);
  if (s->seq != NULL)
    free(s->seq);
  free(s);
}

anchor_t parse_anchor(char *line) {
  anchor_t a;
  int i;
  char *p, *q;
  for (i = 0, p = q = line;; ++p) {
    if (*p == 0 || *p == ':') {
      int c = *p;
      *p = 0;
      /* 0: vertex (as in GFA)
         1: offset
         2: kmer
       */
      if (i == 0) {
        a.v = atoi(q);
      } else if (i == 1) {
        a.offset = atoi(q);
      } else if (i == 2) {
        // char *pEnd;
        a.seq = strtoull(q, NULL /*&pEnd*/, 10);
      }
      ++i;
      q = p + 1;
      if (c == 0)
        break;
    }
  }
  return a;
}

void parse_sfs_line(char *line, sfs_t *s) {
  int i;
  char *p, *q;
  for (i = 0, p = q = line;; ++p) {
    if (*p == 0 || *p == ' ') {
      int c = *p;
      *p = 0;
      /* 0: read idx in .fq
         1: read name
         2: start on read
         3: length
         4: strand
         5: if we kept it
         6: sequence
         7: left anchor
         8: right anchor
       */
      if (i == 0) {
        s->qidx = atoi(q);
      } else if (i == 1) {
        strncpy(s->rname, q, p - q);
        s->rname[p - q] = '\0';
      } else if (i == 2) {
        s->s = atoi(q);
      } else if (i == 3) {
        s->l = atoi(q);
      } else if (i == 4) {
        s->strand = atoi(q);
      } else if (i == 6) {
        // s.seq = (uint8_t *)malloc(s.l + 1);
        // memcpy(s.seq, q, s.l);
        // s.seq[s.l] = '\0';
        // for (int _i = 0; _i < s.l; ++_i)
        //   s.seq[_i] = s.seq[_i] < 128 ? to_int[s.seq[_i]] : 5;
      } else if (i == 7) {
        s->a = parse_anchor(q);
        s->a.p = s->s;
      } else if (i == 8) {
        s->b = parse_anchor(q);
        s->b.p = s->s;
      }
      ++i;
      q = p + 1;
      if (c == 0)
        break;
    }
  }
}