int splicing_genomic_to_iso(const splicing_gff_t *gff, size_t gene,
const splicing_vector_int_t *position,
splicing_matrix_int_t *isopos) {
size_t r, i, noiso, noreads=splicing_vector_int_size(position);
splicing_vector_int_t exstart, exend, exidx, shift;
splicing_gff_noiso_one(gff, gene, &noiso);
SPLICING_CHECK(splicing_vector_int_init(&exstart, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &exstart);
SPLICING_CHECK(splicing_vector_int_init(&exend, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &exend);
SPLICING_CHECK(splicing_vector_int_init(&exidx, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &exidx);
SPLICING_CHECK(splicing_gff_exon_start_end(gff, &exstart, &exend,
&exidx, gene));
SPLICING_CHECK(splicing_vector_int_init(&shift, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &shift);
for (i=0; i<noiso; i++) {
size_t cs=0, ce=0, ex=0;
int pos=VECTOR(exidx)[i], pos2=VECTOR(exidx)[i+1];
while (pos < pos2) {
cs += VECTOR(exstart)[pos];
SPLICING_CHECK(splicing_vector_int_push_back(&shift, cs-ce-ex-1));
ex++; ce += VECTOR(exend)[pos]; pos++;
}
}
SPLICING_CHECK(splicing_matrix_int_resize(isopos, noiso, noreads));
for (r=0; r<noreads; r++) {
for (i=0; i<noiso; i++) {
size_t pos=VECTOR(*position)[r];
size_t startpos=VECTOR(exidx)[i];
size_t endpos=VECTOR(exidx)[i+1];
int ex;
for (ex=startpos; ex < endpos && VECTOR(exend)[ex] < pos; ex++) ;
if (VECTOR(exstart)[ex] <= pos && pos <= VECTOR(exend)[ex]) {
MATRIX(*isopos, i, r) = VECTOR(*position)[r] - VECTOR(shift)[ex];
} else {
MATRIX(*isopos, i, r) = -1;
}
}
}
splicing_vector_int_destroy(&shift);
splicing_vector_int_destroy(&exidx);
splicing_vector_int_destroy(&exend);
splicing_vector_int_destroy(&exstart);
SPLICING_FINALLY_CLEAN(4);
return 0;
}
int splicing_genomic_to_iso(const splicing_gff_t *gff, size_t gene,
const splicing_vector_int_t *position,
const splicing_gff_converter_t *converter,
splicing_matrix_int_t *isopos) {
size_t r, i, noreads=splicing_vector_int_size(position);
splicing_gff_converter_t vconverter,
*myconverter = (splicing_gff_converter_t*) converter;
if (!converter) {
myconverter=&vconverter;
SPLICING_CHECK(splicing_gff_converter_init(gff, gene, myconverter));
SPLICING_FINALLY(splicing_gff_converter_destroy, myconverter);
}
SPLICING_CHECK(splicing_matrix_int_resize(isopos, myconverter->noiso,
noreads));
for (r=0; r<noreads; r++) {
for (i=0; i<myconverter->noiso; i++) {
size_t pos=VECTOR(*position)[r];
size_t startpos=VECTOR(myconverter->exidx)[i];
size_t endpos=VECTOR(myconverter->exidx)[i+1];
int ex;
for (ex=startpos;
ex < endpos && VECTOR(myconverter->exend)[ex] < pos;
ex++) ;
if (ex < endpos && VECTOR(myconverter->exstart)[ex] <= pos &&
pos <= VECTOR(myconverter->exend)[ex]) {
MATRIX(*isopos, i, r) = VECTOR(*position)[r] -
VECTOR(myconverter->shift)[ex];
} else {
MATRIX(*isopos, i, r) = -1;
}
}
}
if (!converter) {
splicing_gff_converter_destroy(myconverter);
SPLICING_FINALLY_CLEAN(1);
}
return 0;
}
