static int gt_index_options_check_set_out_opts(void *oip, GtError *err)
{
int had_err = 0;
GtIndexOptions *oi = (GtIndexOptions*) oip;
gt_assert(oi != NULL && oi->type != GT_INDEX_OPTIONS_UNDEFINED);
gt_error_check(err);
if (!had_err) {
int retval;
retval = gt_readmode_parse(gt_str_get(oi->dir), err);
if (retval < 0) {
had_err = -1;
} else {
oi->readmode = (GtReadmode) retval;
if (oi->type == GT_INDEX_OPTIONS_PACKED
&& (oi->readmode == GT_READMODE_COMPL
|| oi->readmode == GT_READMODE_REVCOMPL)) {
gt_error_set(err,"construction of packed index not possible for "
"complemented and for reverse complemented sequences");
had_err = -1;
}
}
}
if (!had_err && oi->type == GT_INDEX_OPTIONS_PACKED) {
#ifndef S_SPLINT_S
gt_computePackedIndexDefaults(&oi->bwtIdxParams, BWTBaseFeatures);
#endif
}
if (!had_err && gt_option_is_set(oi->optionkys)) {
oi->outkystab = true;
if (strcmp(gt_str_get(oi->kysargumentstring), "sort") == 0) {
oi->outkyssort = true;
} else {
if (strcmp(gt_str_get(oi->kysargumentstring),"nosort") != 0) {
gt_error_set(err,"illegal argument to option -kys: either use no "
"argument or argument \"sort\"");
had_err = -1;
}
}
}
return had_err;
}
int gt_encseq_decode_arguments_check(GT_UNUSED int rest_argc,
void *tool_arguments,
GtError* err)
{
GtEncseqDecodeArguments *args = (GtEncseqDecodeArguments*) tool_arguments;
int had_err = 0;
int rval;
if (gt_str_length(args->dir) > 0) {
rval = gt_readmode_parse(gt_str_get(args->dir), err);
if (rval < 0)
had_err = -1;
else
args->rm = (GtReadmode) rval;
}
if (!had_err && args->seqrng.start != GT_UNDEF_UWORD &&
args->seqrng.end != GT_UNDEF_UWORD && args->seq != GT_UNDEF_UWORD) {
gt_error_set(err, "'-seq' and '-seqrange' cannot be used together");
had_err = -1;
}
if (!had_err && (args->seqrng.start != GT_UNDEF_UWORD ||
args->seqrng.end != GT_UNDEF_UWORD || args->seq != GT_UNDEF_UWORD)
&& strcmp(gt_str_get(args->mode), "fasta") != 0) {
gt_error_set(err, "'-seq' and '-seqrange' can only be used with the "
"'-output fasta' option");
had_err = -1;
}
if (!had_err && (args->rng.start != GT_UNDEF_UWORD ||
args->rng.end != GT_UNDEF_UWORD)
&& strcmp(gt_str_get(args->mode), "concat") != 0) {
gt_error_set(err, "'-range' can only be used with the "
"'-output concat' option");
had_err = -1;
}
return had_err;
}
static int gt_encseq_bitextract_runner(GT_UNUSED int argc, const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments,
GT_UNUSED GtError *err)
{
GtEncseqBitextractArguments *arguments = tool_arguments;
GtEncseqLoader *el;
GtEncseq *encseq;
int had_err = 0;
bool fwd, it1, GT_UNUSED it2;
char buffer[BUFSIZ];
GtEndofTwobitencoding etbe;
GtEncseqReader *esr;
GtSpecialrangeiterator *sri;
GtRange srng;
GtReadmode rm;
gt_error_check(err);
gt_assert(arguments);
el = gt_encseq_loader_new();
encseq = gt_encseq_loader_load(el, argv[parsed_args], err);
if (!encseq)
had_err = -1;
if (!had_err && arguments->mirror) {
had_err = gt_encseq_mirror(encseq, err);
}
if (!had_err) {
rm = gt_readmode_parse(gt_str_get(arguments->readmode), NULL);
fwd = GT_ISDIRREVERSE(rm) ? false : true;
}
if (!had_err && arguments->bitpos != GT_UNDEF_ULONG) {
if (arguments->bitpos >= gt_encseq_total_length(encseq)) {
gt_error_set(err, "position %lu exceeds encoded sequence length of %lu",
arguments->bitpos, gt_encseq_total_length(encseq));
had_err = -1;
}
if (!had_err) {
unsigned long ret;
esr = gt_encseq_create_reader_with_readmode(encseq, rm,
arguments->bitpos);
ret = gt_encseq_extract2bitencwithtwobitencodingstoppos(&etbe, esr,
encseq,
rm, arguments->bitpos);
gt_bitsequence_tostring(buffer, etbe.tbe);
printf("Twobitencoding %s\n"
"unitsnotspecial %u\n"
"position %lu\n"
"returnvalue %lu\n",
buffer,
etbe.unitsnotspecial,
arguments->bitpos,
ret);
gt_encseq_reader_delete(esr);
}
}
if (!had_err && arguments->stoppos != GT_UNDEF_ULONG) {
if (arguments->stoppos >= gt_encseq_total_length(encseq)) {
gt_error_set(err, "position %lu exceeds encoded sequence length of %lu",
arguments->stoppos, gt_encseq_total_length(encseq));
had_err = -1;
}
if (!had_err) {
esr = gt_encseq_create_reader_with_readmode(encseq, rm, 0);
/* check stoppos stuff */
gt_encseq_reader_reinit_with_readmode(esr, encseq, rm,
arguments->stoppos);
printf("%lu: %lu\n", arguments->stoppos,
gt_getnexttwobitencodingstoppos(fwd, esr));
gt_encseq_reader_delete(esr);
}
}
if (!had_err && arguments->specialranges) {
/* check specialrangeiterator stuff */
if (gt_encseq_has_specialranges(encseq)) {
sri = gt_specialrangeiterator_new(encseq, fwd);
while (true) {
it1 = gt_specialrangeiterator_next(sri, &srng);
if (it1)
printf("%lu:%lu\n", srng.start, srng.end);
else break;
}
gt_specialrangeiterator_delete(sri);
}
}
gt_encseq_delete(encseq);
gt_encseq_loader_delete(el);
return had_err;
}
