/* * Compute the visible end position of a contig. This isn't just the extents * of start_used / end_used in the bins as this can included invisible * data such as cached consensus sequences. */ int contig_visible_end(GapIO *io, tg_rec crec) { rangec_t *r; contig_iterator *ci; ci = contig_iter_new_by_type(io, crec, 1, CITER_LAST | CITER_IEND, CITER_CSTART, CITER_CEND, GRANGE_FLAG_ISANY); if (!ci) { contig_t *c = cache_search(io, GT_Contig, crec); return c->end; } while (r = contig_iter_prev(io, ci)) { int v; if ((r->flags & GRANGE_FLAG_ISMASK) == GRANGE_FLAG_ISCONS) continue; v = r->end; contig_iter_del(ci); return v; } contig_iter_del(ci); return 0; }
static void tag_shift_for_delete(GapIO *io, tg_rec crec, tg_rec srec, int start, int end, int pos, tg_rec brec) { contig_iterator *ci; rangec_t *r; contig_t *c = cache_search(io, GT_Contig, crec);; //printf("< tag in seq %"PRIrec" at %d\n", srec, pos); cache_incr(io, c); ci = contig_iter_new_by_type(io, crec, 0, CITER_FIRST | CITER_ISTART, start+pos, end, GRANGE_FLAG_ISANNO); if (!ci) { cache_decr(io, c); return; } while ((r = contig_iter_next(io, ci))) { range_t r2, *r_out; anno_ele_t *a; bin_index_t *bin; if (r->pair_rec != srec) continue; bin_remove_item(io, &c, GT_AnnoEle, r->rec); r2.start = (r->start > start+pos) ? r->start-1 : r->start; r2.end = r->end-1; r2.mqual = r->mqual; r2.rec = r->rec; r2.pair_rec = r->pair_rec; r2.flags = r->flags; if (r2.end < r2.start) { /* Tag entirely removed now, it must have been on a pad */ a = cache_search(io, GT_AnnoEle, r->rec); a = cache_rw(io, a); cache_deallocate(io, a); continue; } bin = bin_add_to_range(io, &c, brec, &r2, &r_out, NULL, 0); a = cache_search(io, GT_AnnoEle, r->rec); if (a->bin != bin->rec /*|| a->idx != r_out - ArrayBase(range_t, bin->rng)*/) { /* Annotation moved bins */ a = cache_rw(io, a); a->bin = bin->rec; //a->bin_idx = r_out - ArrayBase(range_t, bin->rng); } } cache_decr(io, c); contig_iter_del(ci); }
int edview_search_tag_type(edview *xx, int dir, int strand, char *value) { contig_iterator *iter; int start, end; rangec_t *r; rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci); int type = str2type(value); contig_t *c = cache_search(xx->io, GT_Contig, xx->cnum); if (dir) { start = xx->cursor_apos + (dir ? 1 : -1); end = c->end; ifunc = contig_iter_next; } else { start = c->start; end = xx->cursor_apos + (dir ? 1 : -1); ifunc = contig_iter_prev; } iter = contig_iter_new_by_type(xx->io, xx->cnum, 1, dir == 1 ? CITER_FIRST : CITER_LAST, start, end, GRANGE_FLAG_ISANNO); if (!iter) /* Can happen legitimately when we're already at the end of contig */ return -1; while (r = ifunc(xx->io, iter)) { if ((dir && r->start < start) || (!dir && r->start > end)) continue; if (r->mqual == type) break; } if (r) { if (r->flags & GRANGE_FLAG_TAG_SEQ) { int pos; sequence_get_position(xx->io, r->pair_rec, NULL, &pos, NULL, NULL); pos = r->start - pos; edSetCursorPos(xx, GT_Seq, r->pair_rec, pos, 1); } else { edSetCursorPos(xx, GT_Contig, xx->cnum, r->start, 1); } contig_iter_del(iter); return 0; } contig_iter_del(iter); return -1; }
int edview_search_tag_indel(edview *xx, int dir, int strand, char *value) { contig_iterator *iter; int start, end; rangec_t *r; rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci); contig_t *c = cache_search(xx->io, GT_Contig, xx->cnum); if (dir) { start = xx->cursor_apos + (dir ? 1 : -1); end = c->end; ifunc = contig_iter_next; } else { start = c->start; end = xx->cursor_apos + (dir ? 1 : -1); ifunc = contig_iter_prev; } iter = contig_iter_new_by_type(xx->io, xx->cnum, 1, dir == 1 ? CITER_FIRST : CITER_LAST, start, end, GRANGE_FLAG_ISREFPOS); if (!iter) return -1; while (r = ifunc(xx->io, iter)) { if ((dir && r->start < start) || (!dir && r->start > end)) continue; break; } if (r) { edSetCursorPos(xx, GT_Contig, xx->cnum, r->start, 1); contig_iter_del(iter); return 0; } contig_iter_del(iter); return -1; }
/* * Removes all tags of specific types (hashed in h, or all if h == NULL) * from a specified contig. * * Returns 0 on success * -1 on failure */ static int delete_tag_single_contig(GapIO *io, tg_rec crec, HashTable *h, int verbose) { contig_iterator *ci; rangec_t *r; contig_t *c; int ret = -1; ci = contig_iter_new_by_type(io, crec, 1, CITER_FIRST, CITER_CSTART, CITER_CEND, GRANGE_FLAG_ISANNO); if (!ci) return -1; if (!(c = cache_search(io, GT_Contig, crec))) { contig_iter_del(ci); return -1; } cache_incr(io, c); while (NULL != (r = contig_iter_next(io, ci))) { char t[5]; (void)type2str(r->mqual, t); if (!h || HashTableSearch(h, t, 4)) { anno_ele_t *e; if (verbose) vmessage("Removing anno %s #%"PRIrec"\tContig %s\t%d..%d\n", t, r->rec, c->name, r->start, r->end); if (bin_remove_item(io, &c, GT_AnnoEle, r->rec)) goto fail; /* FIXME: Need to reclaim the GT_AnnoEle record itself */ } } ret = 0; fail: contig_iter_del(ci); cache_decr(io, c); return ret; }
int edview_search_tag_anno(edview *xx, int dir, int strand, char *value) { contig_iterator *iter; int start, end; rangec_t *r; rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci); char *r_exp = NULL; contig_t *c = cache_search(xx->io, GT_Contig, xx->cnum); if (value) { if (NULL == (r_exp = REGCMP(xx->interp, value))) { verror(ERR_WARN, "Search by anno", "invalid regular expression"); return -1; } } if (dir) { start = xx->cursor_apos + (dir ? 1 : -1); end = c->end; ifunc = contig_iter_next; } else { start = c->start; end = xx->cursor_apos + (dir ? 1 : -1); ifunc = contig_iter_prev; } iter = contig_iter_new_by_type(xx->io, xx->cnum, 1, dir == 1 ? CITER_FIRST : CITER_LAST, start, end, GRANGE_FLAG_ISANNO); if (!iter) return -1; while (r = ifunc(xx->io, iter)) { anno_ele_t *ae; if ((dir && r->start < start) || (!dir && r->start > end)) continue; if (!r_exp) break; /* blank expr => match all */ ae = cache_search(xx->io, GT_AnnoEle, r->rec); if (!ae->comment) continue; if (REGEX(xx->interp, ae->comment, r_exp)) break; } REGFREE(xx->interp, r_exp); if (r) { if (r->flags & GRANGE_FLAG_TAG_SEQ) { int pos; sequence_get_position(xx->io, r->pair_rec, NULL, &pos, NULL, NULL); pos = r->start - pos; edSetCursorPos(xx, GT_Seq, r->pair_rec, pos, 1); } else { edSetCursorPos(xx, GT_Contig, xx->cnum, r->start, 1); } contig_iter_del(iter); return 0; } contig_iter_del(iter); return -1; }
int edview_search_name(edview *xx, int dir, int strand, char *value) { tg_rec rec, *rp, cnum = -1, best_rec; int best_pos, best_off; int nr, i; rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci); int start, end, cstart; contig_iterator *iter; contig_t *c; /* Check for #num where num is a sequence record in this contig */ if (*value == '#') { char *endp; int64_t v = strtol64(value+1, &endp, 10); rec = v; if (*endp == '\0' && cache_exists(xx->io, GT_Seq, rec)) { sequence_get_clipped_position(xx->io, rec, &cnum, &start, NULL, &cstart, NULL, NULL); if (cnum == xx->cnum) { edSetCursorPos(xx, GT_Seq, rec, cstart - start, 1); return 0; } } } /* Find all hits matching this name */ rp = sequence_index_query_all(xx->io, value, 1, &nr); /* Also get an position-based iterator */ c = cache_search(xx->io, GT_Contig, xx->cnum); if (dir) { start = xx->cursor_apos + 1; end = c->end; ifunc = contig_iter_next; best_pos = end + 1; best_off = 0; } else { start = c->start; end = xx->cursor_apos - 1; ifunc = contig_iter_prev; best_pos = start - 1; best_off = 0; } iter = contig_iter_new_by_type(xx->io, xx->cnum, 1, dir == 1 ? CITER_FIRST : CITER_LAST, start-1, end+1, GRANGE_FLAG_ISSEQ); if (!iter) return -1; /* * The iterator also finds overlapping objects, not just ones beyond this * point. That's fine if we're on the consensus as we probably want to * jump to the first seq-name overlapping this point. * * However if we're on a sequence already, we want the first one * after or before that sequence. So we skip along iterator until we're * at the current record. */ if (xx->cursor_type == GT_Seq) { rangec_t *r; while ((r = ifunc(xx->io, iter))) { if (r->rec == xx->cursor_rec) break; } } /* Alternate between the by-name and by-position scan */ best_rec = -1; for (i = 0; i < nr; i++) { int start, end; rangec_t *r; /* From name index */ rec = rp[i++]; sequence_get_clipped_position(xx->io, rec, &cnum, &start, &end, &cstart, NULL, NULL); if (cnum == xx->cnum) { if ((dir && best_pos > cstart && cstart > xx->cursor_apos) || (!dir && best_pos < cstart && cstart < xx->cursor_apos)) { best_pos = cstart; best_off = cstart - start; best_rec = rec; } } /* From iterator */ if ((r = ifunc(xx->io, iter))) { seq_t *s; if (NULL == (s = cache_search(xx->io, GT_Seq, r->rec))) { /* No match */ best_rec = -1; break; } if (strncmp(s->name, value, strlen(value)) == 0) { /* prefix match */ puts("Found by pos iterator"); best_rec = r->rec; break; } } else { /* End of contig - bail out early */ best_rec = -1; break; } } contig_iter_del(iter); if (rp) free(rp); if (best_rec != -1) { edSetCursorPos(xx, GT_Seq, best_rec, best_off, 1); return 0; } return -1; }