static void showmatch(void *processinfo,const GtMatch *match)
{
Showmatchinfo *showmatchinfo = (Showmatchinfo *) processinfo;
unsigned long seqnum;
Seqpos relpos;
if (match->dbabsolute)
{
Seqinfo seqinfo;
seqnum = getencseqfrompos2seqnum(showmatchinfo->encseq,match->dbstartpos);
getencseqSeqinfo(&seqinfo,showmatchinfo->encseq,seqnum);
gt_assert(seqinfo.seqstartpos <= match->dbstartpos);
relpos = match->dbstartpos - seqinfo.seqstartpos;
} else
{
relpos = match->dbstartpos;
seqnum = match->dbseqnum;
}
printf("%lu\t" FormatSeqpos "\t",seqnum,PRINTSeqposcast(relpos));
printf(FormatSeqpos "\t",PRINTSeqposcast(match->dblen));
printf("\t" Formatuint64_t "\t%lu\t%lu\t%lu\n",
PRINTuint64_tcast(showmatchinfo->queryunit),
match->querystartpos,
match->querylen,
match->distance);
if (showmatchinfo->showalignment)
{
gt_alignment_show_with_mapped_chars(
(const GtAlignment *) match->alignment,
showmatchinfo->characters,
showmatchinfo->wildcardshow,
stdout);
}
}
void showinfoiffoundfullLTRs(const LTRharvestoptions *lo,
const LTRboundaries **bdptrtab,
unsigned long numofboundaries,
const Encodedsequence *encseq)
{
Seqinfo seqinfo;
unsigned long i;
if (lo->longoutput)
{
if (numofboundaries == 0)
{
printf("No full LTR-pair predicted.\n");
} else
{
printlongheader(lo);
/* print output sorted by contignumber*/
for (i = 0; i<numofboundaries; i++)
{
getencseqSeqinfo(&seqinfo,encseq,bdptrtab[i]->contignumber);
producelongutput(lo,
bdptrtab[i],
encseq,
seqinfo.seqstartpos);
}
}
} else
{
if (numofboundaries > 0)
{
printshortheader();
/* print output sorted by contignumber*/
for (i = 0; i<numofboundaries; i++)
{
getencseqSeqinfo(&seqinfo,encseq,bdptrtab[i]->contignumber);
produceshortoutput(bdptrtab[i],seqinfo.seqstartpos);
}
}
}
}
