void gt_queryuniquematch(bool selfmatch,
const Suffixarray *suffixarray,
uint64_t queryunitnum,
GtQueryrepresentation *queryrep,
GtUword minmatchlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtQuerymatch *querymatchspaceptr)
{
GtUword offset, totallength = gt_encseq_total_length(suffixarray->encseq),
localqueryoffset = 0;
uint64_t localqueryunitnum = queryunitnum;
gt_assert(!selfmatch && queryrep->seqlen >= minmatchlength);
for (offset = 0; offset <= queryrep->seqlen - minmatchlength; offset++)
{
GtUword matchlen, dbstart;
matchlen = gt_suffixarrayfindmums (suffixarray,
0,
0, /* leftbound */
totallength, /* rightbound */
&dbstart,
queryrep->sequence + offset,
queryrep->sequence + queryrep->seqlen);
if (dbstart != ULONG_MAX &&
matchlen >= minmatchlength &&
gt_mum_isleftmaximal(suffixarray->encseq,
suffixarray->readmode,
dbstart,
offset,
queryrep->sequence))
{
GtUword dbseqnum = gt_encseq_seqnum(suffixarray->encseq,dbstart),
dbseqstartpos = gt_encseq_seqstartpos(suffixarray->encseq,
dbseqnum),
dbseqlen = gt_encseq_seqlength(suffixarray->encseq,dbseqnum);
gt_querymatch_init(querymatchspaceptr,
matchlen,
dbstart,
dbseqnum,
dbstart - dbseqstartpos,
dbseqlen,
0, /* score */
0, /* edist */
selfmatch,
localqueryunitnum,
matchlen,
localqueryoffset,
queryrep->seqlen);
processquerymatch(processquerymatchinfo,querymatchspaceptr);
}
if (queryrep->sequence[offset] == (GtUchar) SEPARATOR)
{
localqueryunitnum++;
localqueryoffset = 0;
} else
{
localqueryoffset++;
}
}
}
static int gt_queryuniquematch(bool selfmatch,
const Suffixarray *suffixarray,
uint64_t queryunitnum,
const GtQueryrep *queryrep,
unsigned long minmatchlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtQuerymatch *querymatchspaceptr,
GtError *err)
{
unsigned long offset,
totallength = gt_encseq_total_length(suffixarray->encseq),
localqueryoffset = 0;
uint64_t localqueryunitnum = queryunitnum;
bool haserr = false;
gt_assert(!selfmatch && queryrep->length >= minmatchlength);
for (offset = 0; offset <= queryrep->length - minmatchlength; offset++)
{
unsigned long matchlen, dbstart;
matchlen = gt_suffixarrayfindmums (suffixarray,
0,
0, /* leftbound */
totallength, /* rightbound */
&dbstart,
queryrep->sequence + offset,
queryrep->sequence + queryrep->length);
if (dbstart != ULONG_MAX &&
matchlen >= minmatchlength &&
gt_mum_isleftmaximal(suffixarray->encseq,
suffixarray->readmode,
dbstart,
offset,
queryrep->sequence))
{
gt_querymatch_fill(querymatchspaceptr,
matchlen,
dbstart,
queryrep->readmode,
queryrep->reversecopy,
0, /* score */
0, /* edist */
selfmatch,
localqueryunitnum,
matchlen,
localqueryoffset);
if (processquerymatch(processquerymatchinfo,
suffixarray->encseq,
querymatchspaceptr,
queryrep->sequence,
queryrep->length,
err) != 0)
{
haserr = true;
}
}
if (!haserr)
{
if (queryrep->sequence[offset] == (GtUchar) SEPARATOR)
{
localqueryunitnum++;
localqueryoffset = 0;
} else
{
localqueryoffset++;
}
}
}
return haserr ? -1 : 0;
}
