/* --- .Call ENTRY POINT --- */
SEXP write_XStringSet_to_fasta(SEXP x, SEXP filexp_list, SEXP width, SEXP lkup)
{
XStringSet_holder X;
int x_length, width0, lkup_length, i, j1, j2, dest_nbytes;
const int *lkup0;
SEXP filexp, x_names, desc;
Chars_holder X_elt;
char buf[IOBUF_SIZE];
X = _hold_XStringSet(x);
x_length = _get_length_from_XStringSet_holder(&X);
filexp = VECTOR_ELT(filexp_list, 0);
width0 = INTEGER(width)[0];
if (width0 >= IOBUF_SIZE)
error("'width' must be <= %d", IOBUF_SIZE - 1);
buf[width0] = 0;
if (lkup == R_NilValue) {
lkup0 = NULL;
lkup_length = 0;
} else {
lkup0 = INTEGER(lkup);
lkup_length = LENGTH(lkup);
}
x_names = get_XVectorList_names(x);
for (i = 0; i < x_length; i++) {
filexp_puts(filexp, FASTA_desc_markup);
if (x_names != R_NilValue) {
desc = STRING_ELT(x_names, i);
if (desc == NA_STRING)
error("'names(x)' contains NAs");
filexp_puts(filexp, CHAR(desc));
}
filexp_puts(filexp, "\n");
X_elt = _get_elt_from_XStringSet_holder(&X, i);
for (j1 = 0; j1 < X_elt.length; j1 += width0) {
j2 = j1 + width0;
if (j2 > X_elt.length)
j2 = X_elt.length;
dest_nbytes = j2 - j1;
j2--;
Ocopy_bytes_from_i1i2_with_lkup(j1, j2,
buf, dest_nbytes,
X_elt.ptr, X_elt.length,
lkup0, lkup_length);
buf[dest_nbytes] = 0;
filexp_puts(filexp, buf);
filexp_puts(filexp, "\n");
}
}
return R_NilValue;
}
/* --- .Call ENTRY POINT --- */
SEXP write_XStringSet_to_fastq(SEXP x, SEXP filexp_list,
SEXP qualities, SEXP lkup)
{
XStringSet_holder X, Q;
int x_length, lkup_length, i;
const int *lkup0;
SEXP filexp, x_names, q_names;
const char *id;
Chars_holder X_elt;
char buf[IOBUF_SIZE];
X = _hold_XStringSet(x);
x_length = _get_length_from_XStringSet_holder(&X);
if (qualities != R_NilValue) {
Q = _hold_XStringSet(qualities);
if (_get_length_from_XStringSet_holder(&Q) != x_length)
error("'x' and 'qualities' must have the same length");
q_names = get_XVectorList_names(qualities);
} else {
q_names = R_NilValue;
}
filexp = VECTOR_ELT(filexp_list, 0);
if (lkup == R_NilValue) {
lkup0 = NULL;
lkup_length = 0;
} else {
lkup0 = INTEGER(lkup);
lkup_length = LENGTH(lkup);
}
x_names = get_XVectorList_names(x);
for (i = 0; i < x_length; i++) {
id = get_FASTQ_rec_id(x_names, q_names, i);
X_elt = _get_elt_from_XStringSet_holder(&X, i);
Ocopy_bytes_from_i1i2_with_lkup(0, X_elt.length - 1,
buf, X_elt.length,
X_elt.ptr, X_elt.length,
lkup0, lkup_length);
buf[X_elt.length] = 0;
write_FASTQ_id(filexp, FASTQ_line1_markup, id);
write_FASTQ_seq(filexp, buf);
write_FASTQ_id(filexp, FASTQ_line3_markup, id);
if (qualities != R_NilValue) {
write_FASTQ_qual(filexp, X_elt.length, &Q, i);
} else {
write_FASTQ_fakequal(filexp, X_elt.length);
}
}
return R_NilValue;
}
static int copy_exon(char * out, const cachedCharSeq *in,
int start, int end, int on_minus_strand, SEXP lkup)
{
int width;
start--; end--;
width = end - start + 1;
if (on_minus_strand) {
Orevcopy_bytes_from_i1i2_with_lkup(start, end,
out, width,
in->seq, in->length,
INTEGER(lkup), LENGTH(lkup));
} else {
Ocopy_bytes_from_i1i2_with_lkup(start, end,
out, width,
in->seq, in->length,
NULL, 0);
}
return width;
}
