static void singleseqtyrsearch(const Tyrindex *tyrindex,
const Tyrcountinfo *tyrcountinfo,
const Tyrsearchinfo *tyrsearchinfo,
const Tyrbckinfo *tyrbckinfo,
uint64_t unitnum,
const GtUchar *query,
unsigned long querylen,
GT_UNUSED const char *desc)
{
const GtUchar *qptr, *result;
unsigned long offset, skipvalue;
if (tyrsearchinfo->mersize > querylen)
{
return;
}
qptr = query;
offset = 0;
while (qptr <= query + querylen - tyrsearchinfo->mersize)
{
skipvalue = containsspecialbytestring(qptr,offset,tyrsearchinfo->mersize);
if (skipvalue == tyrsearchinfo->mersize)
{
offset = tyrsearchinfo->mersize-1;
if (tyrsearchinfo->searchstrand & STRAND_FORWARD)
{
result = gt_searchsinglemer(qptr,tyrindex,tyrsearchinfo,tyrbckinfo);
if (result != NULL)
{
mermatchoutput(tyrindex,
tyrcountinfo,
tyrsearchinfo,
result,
query,
qptr,
unitnum,
true);
}
}
if (tyrsearchinfo->searchstrand & STRAND_REVERSE)
{
gt_assert(tyrsearchinfo->rcbuf != NULL);
gt_copy_reversecomplement(tyrsearchinfo->rcbuf,qptr,
tyrsearchinfo->mersize);
result = gt_searchsinglemer(tyrsearchinfo->rcbuf,tyrindex,
tyrsearchinfo,tyrbckinfo);
if (result != NULL)
{
mermatchoutput(tyrindex,
tyrcountinfo,
tyrsearchinfo,
result,
query,
qptr,
unitnum,
false);
}
}
qptr++;
} else
{
offset = 0;
qptr += (skipvalue+1);
}
}
}
static int gt_callenumquerymatches_withindex(
GtQuerysubstringmatchfunc findquerymatches,
const Suffixarray *suffixarray,
const GtStrArray *queryfiles,
bool forwardstrand,
bool reversestrand,
unsigned int userdefinedleastlength,
GtProcessquerybeforematching
processquerybeforematching,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtError *err)
{
GtSeqIterator *seqit;
bool haserr = false;
seqit = gt_seq_iterator_sequence_buffer_new(queryfiles, err);
if (seqit == NULL)
{
haserr = true;
} else
{
GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
const GtUchar *query;
unsigned long querylen;
int retval;
uint64_t queryunitnum;
GtUchar *queryreverse = NULL;
unsigned long queryreverse_length = 0;
char *desc = NULL;
int mode;
gt_seq_iterator_set_symbolmap(seqit,
gt_alphabet_symbolmap(gt_encseq_alphabet(
suffixarray->encseq)));
for (queryunitnum = 0; /* Nothing */; queryunitnum++)
{
retval = gt_seq_iterator_next(seqit, &query, &querylen, &desc, err);
if (retval < 0)
{
haserr = true;
break;
}
if (retval == 0)
{
break;
}
if (querylen >= (unsigned long) userdefinedleastlength)
{
GtQueryrep queryrep;
queryrep.encseq = NULL;
queryrep.readmode = GT_READMODE_FORWARD;
queryrep.startpos = 0;
queryrep.length = querylen;
for (mode = 0; mode <= 1; mode++)
{
if (mode == 0 && forwardstrand)
{
queryrep.sequence = query;
queryrep.reversecopy = false;
if (processquerybeforematching != NULL)
{
processquerybeforematching(processquerymatchinfo,desc,query,
querylen,true);
}
} else
{
if (mode == 1 && reversestrand)
{
if (querylen > queryreverse_length)
{
queryreverse = gt_realloc(queryreverse,
sizeof (*queryreverse) * querylen);
queryreverse_length = querylen;
}
gt_copy_reversecomplement(queryreverse,query,querylen);
queryrep.sequence = queryreverse;
queryrep.reversecopy = true;
if (processquerybeforematching != NULL)
{
processquerybeforematching(processquerymatchinfo,desc,
queryreverse,querylen,false);
}
} else
{
queryrep.sequence = NULL;
queryrep.reversecopy = false;
}
}
if (queryrep.sequence != NULL)
{
int ret = findquerymatches(false,
suffixarray,
queryunitnum,
&queryrep,
(unsigned long) userdefinedleastlength,
processquerymatch,
processquerymatchinfo,
querymatchspaceptr,
err);
if (ret != 0)
{
haserr = true;
break;
}
}
}
}
}
gt_seq_iterator_delete(seqit);
gt_free(queryreverse);
gt_querymatch_delete(querymatchspaceptr);
}
return haserr ? -1 : 0;
}