MatchBuf _new_MatchBuf(int ms_code, int nPSpair)
{
int count_only;
static MatchBuf match_buf;
if (ms_code != MATCHES_AS_NULL
&& ms_code != MATCHES_AS_WHICH
&& ms_code != MATCHES_AS_COUNTS
&& ms_code != MATCHES_AS_STARTS
&& ms_code != MATCHES_AS_ENDS
&& ms_code != MATCHES_AS_RANGES)
error("Biostrings internal error in _new_MatchBuf(): ",
"%d: unsupported match storing code", ms_code);
count_only = ms_code == MATCHES_AS_WHICH ||
ms_code == MATCHES_AS_COUNTS;
match_buf.ms_code = ms_code;
match_buf.PSlink_ids = new_IntAE(0, 0, 0);
match_buf.match_counts = new_IntAE(nPSpair, nPSpair, 0);
if (count_only) {
/* No match_starts and match_widths buffers in that case */
match_buf.match_starts = NULL;
match_buf.match_widths = NULL;
} else {
match_buf.match_starts = new_IntAEAE(nPSpair, nPSpair);
match_buf.match_widths = new_IntAEAE(nPSpair, nPSpair);
}
return match_buf;
}
static FASTAINDEX_loaderExt new_FASTAINDEX_loaderExt()
{
FASTAINDEX_loaderExt loader_ext;
loader_ext.recno_buf = new_IntAE(0, 0, 0);
loader_ext.offset_buf = new_LLongAE(0, 0, 0);
loader_ext.desc_buf = new_CharAEAE(0, 0);
loader_ext.seqlength_buf = new_IntAE(0, 0, 0);
return loader_ext;
}
/* --- .Call ENTRY POINT --- */
SEXP fasta_index(SEXP filexp_list,
SEXP nrec, SEXP skip, SEXP seek_first_rec, SEXP lkup)
{
int nrec0, skip0, seek_rec0, i, recno, old_nrec, new_nrec, k;
FASTAINDEX_loaderExt loader_ext;
FASTAloader loader;
IntAE *seqlength_buf, *fileno_buf;
SEXP filexp;
long long int offset, ninvalid;
const char *errmsg;
nrec0 = INTEGER(nrec)[0];
skip0 = INTEGER(skip)[0];
seek_rec0 = LOGICAL(seek_first_rec)[0];
loader_ext = new_FASTAINDEX_loaderExt();
loader = new_FASTAINDEX_loader(lkup, 1, &loader_ext);
seqlength_buf = loader_ext.seqlength_buf;
fileno_buf = new_IntAE(0, 0, 0);
for (i = recno = 0; i < LENGTH(filexp_list); i++) {
filexp = VECTOR_ELT(filexp_list, i);
offset = ninvalid = 0LL;
errmsg = parse_FASTA_file(filexp, nrec0, skip0, seek_rec0,
&loader, &recno, &offset, &ninvalid);
if (errmsg != NULL)
error("reading FASTA file %s: %s",
CHAR(STRING_ELT(GET_NAMES(filexp_list), i)),
errmsg_buf);
if (ninvalid != 0LL)
warning("reading FASTA file %s: ignored %lld "
"invalid one-letter sequence codes",
CHAR(STRING_ELT(GET_NAMES(filexp_list), i)),
ninvalid);
old_nrec = IntAE_get_nelt(fileno_buf);
new_nrec = IntAE_get_nelt(seqlength_buf);
for (k = old_nrec; k < new_nrec; k++)
IntAE_insert_at(fileno_buf, k, i + 1);
}
return make_fasta_index_data_frame(loader_ext.recno_buf,
fileno_buf,
loader_ext.offset_buf,
loader_ext.desc_buf,
seqlength_buf);
}
