int splicing_i_gff_exon_start_end_sort(const splicing_vector_int_t *start,
const splicing_vector_int_t *end,
const splicing_vector_int_t *idx,
int iso, splicing_vector_int_t *tmp,
splicing_vector_int_t *tmp2) {
int i, j, from=VECTOR(*idx)[iso], to=VECTOR(*idx)[iso+1], len=to-from;
SPLICING_CHECK(splicing_vector_int_resize(tmp, len));
SPLICING_CHECK(splicing_vector_int_resize(tmp2, len));
for (i=0; i<len; i++) { VECTOR(*tmp)[i]=i; }
splicing_qsort_r(VECTOR(*tmp), len, sizeof(int),
(void*) (VECTOR(*start)+from),
splicing_i_gff_exon_start_end_sort_cmp);
/* Store the order */
for (i=0, j=from; i<len; i++, j++) { VECTOR(*tmp2)[i]=VECTOR(*start)[j]; }
for (i=0, j=from; i<len; i++, j++) {
VECTOR(*start)[j] = VECTOR(*tmp2)[ VECTOR(*tmp)[i] ];
}
for (i=0, j=from; i<len; i++, j++) { VECTOR(*tmp2)[i]=VECTOR(*end)[j]; }
for (i=0, j=from; i<len; i++, j++) {
VECTOR(*end)[j] = VECTOR(*tmp2)[ VECTOR(*tmp)[i] ];
}
return 0;
}
int splicing_gff_reindex(splicing_gff_t *gff) {
splicing_vector_int_t index;
splicing_vector_int_t index2;
splicing_vector_int_t gindex;
int i, j, k, n=gff->n;
SPLICING_CHECK(splicing_vector_int_init(&index, n));
SPLICING_FINALLY(splicing_vector_int_destroy, &index);
for (i=0; i<n; i++) { VECTOR(index)[i] = i; }
splicing_qsort_r(VECTOR(index), n, sizeof(int), (void*) gff,
splicing_i_gff_reindex_cmp);
SPLICING_CHECK(splicing_vector_int_init(&gindex, gff->nogenes));
SPLICING_FINALLY(splicing_vector_int_destroy, &gindex);
SPLICING_CHECK(splicing_vector_int_init(&index2, n));
SPLICING_FINALLY(splicing_vector_int_destroy, &index2);
for (i=0; i<gff->nogenes; i++) {
VECTOR(index2)[ VECTOR(gff->genes)[i] ] = i;
}
for (i=0, j=0; i<n; i++) {
if (VECTOR(gff->type)[ VECTOR(index)[i] ] == SPLICING_TYPE_GENE) {
VECTOR(gindex)[j++] = VECTOR(index2)[ VECTOR(index)[i] ];
}
}
splicing_vector_int_destroy(&index2);
SPLICING_FINALLY_CLEAN(1);
splicing_vector_int_intiindex(&gff->seqid, &gindex);
splicing_vector_int_intiindex(&gff->source, &gindex);
splicing_vector_int_intiindex(&gff->strand, &gindex);
splicing_vector_int_destroy(&gindex);
SPLICING_FINALLY_CLEAN(1);
splicing_vector_int_intiindex(&gff->type, &index);
splicing_vector_int_intiindex(&gff->start, &index);
splicing_vector_int_intiindex(&gff->end, &index);
splicing_vector_intiindex(&gff->score, &index);
splicing_vector_int_intiindex(&gff->phase, &index);
splicing_strvector_ipermute(&gff->ID, &index);
splicing_vector_int_intiindex(&gff->parent, &index);
SPLICING_CHECK(splicing_vector_int_init(&index2, n));
SPLICING_FINALLY(splicing_vector_int_destroy, &index2);
for (i=0; i<n; i++) {
VECTOR(index2)[ VECTOR(index)[i] ] = i;
}
for (i=0; i<n; i++) {
int p=VECTOR(gff->parent)[i];
if (p != -1) {
VECTOR(gff->parent)[i] = VECTOR(index2)[p];
}
}
splicing_vector_int_destroy(&index2);
SPLICING_FINALLY_CLEAN(1);
for (i=j=k=0; i<n; i++) {
if (VECTOR(gff->type)[i] == SPLICING_TYPE_GENE) {
VECTOR(gff->genes)[j++] = i;
} else if (VECTOR(gff->type)[i] == SPLICING_TYPE_MRNA) {
VECTOR(gff->transcripts)[k++] = i;
}
}
splicing_vector_int_destroy(&index);
SPLICING_FINALLY_CLEAN(1);
return 0;
}
