int test_trieins(bool onlyins,const GtStr *indexname,GtError *err)
{
Suffixarray suffixarray;
bool haserr = false;
Seqpos totallength = 0;
gt_error_check(err);
if (streamsuffixarray(&suffixarray,
SARR_ESQTAB,
indexname,
NULL,
err) != 0)
{
haserr = true;
} else
{
totallength = getencseqtotallength(suffixarray.encseq);
}
if (!haserr)
{
Mergertrierep trierep;
const GtUchar *characters;
ALLOCASSIGNSPACE(trierep.encseqreadinfo,NULL,Encseqreadinfo,1);
trierep.encseqreadinfo[0].encseqptr = suffixarray.encseq;
trierep.encseqreadinfo[0].readmode = suffixarray.readmode;
characters = getencseqAlphabetcharacters(suffixarray.encseq);
mergertrie_initnodetable(&trierep,totallength,1U);
maketrie(&trierep,characters,totallength);
if (onlyins)
{
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
showtrie(&trierep,characters);
#endif
checktrie(&trierep,totallength+1,totallength,err);
#endif
} else
{
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
showallnoderelations(trierep.root);
#endif
#endif
successivelydeletesmallest(&trierep,totallength,characters,err);
}
mergertrie_delete(&trierep);
}
freesuffixarray(&suffixarray);
return haserr ? -1 : 0;
}
static void showexpandcode(const GtBucketspec2 *bucketspec2,
unsigned int prefixlength)
{
Codetype ecode, code2;
const GtUchar *characters = getencseqAlphabetcharacters(bucketspec2->encseq);
for (code2 = 0; code2 < (Codetype) bucketspec2->numofcharssquared; code2++)
{
char buffer[100];
ecode = expandtwocharcode(code2,bucketspec2);
fromkmercode2string(buffer,
ecode,
bucketspec2->numofchars,
prefixlength,
(const char *) characters);
printf("code2=%u = %lu %s\n",(unsigned int) code2,ecode,buffer);
}
}
static void producelongutput(const LTRharvestoptions *lo,
const LTRboundaries *boundaries,
const Encodedsequence *encseq,
Seqpos offset)
{
const GtUchar *characters = getencseqAlphabetcharacters(encseq);
printf(FormatSeqpos " ",
PRINTSeqposcast(boundaries->leftLTR_5 -offset + 1));
printf(FormatSeqpos " ",
PRINTSeqposcast(boundaries->rightLTR_3 -offset + 1));
printf(FormatSeqpos " ",
PRINTSeqposcast((boundaries->rightLTR_3 - boundaries->leftLTR_5
+ 1)));
printf(FormatSeqpos " ",
PRINTSeqposcast(boundaries->leftLTR_5 -offset + 1));
printf(FormatSeqpos " ",
PRINTSeqposcast(boundaries->leftLTR_3 -offset + 1));
printf(FormatSeqpos " ",
PRINTSeqposcast((boundaries->leftLTR_3 - boundaries->leftLTR_5
+ 1)));
if (lo->minlengthTSD > 1U)
{
Seqpos j;
for (j = 0; j < boundaries->lenleftTSD; j++)
{
printf("%c",(char) characters[getencodedchar(encseq,
boundaries->leftLTR_5 -
boundaries->lenleftTSD + j,
Forwardmode)]);
}
printf(" " FormatSeqpos " ",
PRINTSeqposcast(boundaries->lenleftTSD));
}
if (lo->motif.allowedmismatches < 4U)
{
printf("%c%c..%c%c ",
(char) characters[getencodedchar(encseq,/* Random access */
boundaries->leftLTR_5,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Random access */
boundaries->leftLTR_5+1,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Random access */
boundaries->leftLTR_3-1,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Random access */
boundaries->leftLTR_3,
Forwardmode)] );
}
/* increase by 1 */
printf(FormatSeqpos " ",
PRINTSeqposcast(boundaries->rightLTR_5 -offset + 1));
/* increase by 1 */
printf(FormatSeqpos " ",PRINTSeqposcast(boundaries->rightLTR_3 -offset + 1));
printf(FormatSeqpos " ",PRINTSeqposcast(boundaries->rightLTR_3
- boundaries->rightLTR_5 + 1));
if (lo->minlengthTSD > 1U)
{
Seqpos j;
for (j = 0; j < boundaries->lenrightTSD; j++)
{
printf("%c", (char) characters[getencodedchar(encseq,
boundaries->rightLTR_3+j+1,
Forwardmode)]);
}
printf(" " FormatSeqpos " ",PRINTSeqposcast(boundaries->lenrightTSD));
}
if (lo->motif.allowedmismatches < 4U)
{
printf("%c%c..%c%c",
(char) characters[getencodedchar(encseq,/* Randomaccess */
boundaries->rightLTR_5,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Randomaccess */
boundaries->rightLTR_5+1,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Randomaccess */
boundaries->rightLTR_3-1,
Forwardmode)],
(char) characters[getencodedchar(encseq,/* Random access */
boundaries->rightLTR_3,/* Randomaccess */
Forwardmode)] );
}
/* print similarity */
printf(" %.2f", boundaries->similarity);
/* print sequence number */
printf(" %lu\n", boundaries->contignumber);
}
int runidxlocali(const IdxlocaliOptions *idxlocalioptions,GtError *err)
{
Genericindex *genericindex = NULL;
bool haserr = false;
Verboseinfo *verboseinfo;
const Encodedsequence *encseq = NULL;
verboseinfo = newverboseinfo(idxlocalioptions->verbose);
if (idxlocalioptions->doonline)
{
encseq = mapencodedsequence (true,
idxlocalioptions->indexname,
true,
false,
false,
true,
verboseinfo,
err);
if (encseq == NULL)
{
haserr = true;
}
} else
{
genericindex = genericindex_new(idxlocalioptions->indexname,
idxlocalioptions->withesa,
idxlocalioptions->withesa ||
idxlocalioptions->docompare,
false,
true,
0,
verboseinfo,
err);
if (genericindex == NULL)
{
haserr = true;
} else
{
encseq = genericindex_getencseq(genericindex);
}
}
if (!haserr)
{
GtSeqIterator *seqit;
const GtUchar *query;
unsigned long querylen;
char *desc = NULL;
int retval;
Limdfsresources *limdfsresources = NULL;
const AbstractDfstransformer *dfst;
SWdpresource *swdpresource = NULL;
Showmatchinfo showmatchinfo;
Processmatch processmatch;
void *processmatchinfoonline, *processmatchinfooffline;
Storematchinfo storeonline, storeoffline;
if (idxlocalioptions->docompare)
{
processmatch = storematch;
initstorematch(&storeonline,encseq);
initstorematch(&storeoffline,encseq);
processmatchinfoonline = &storeonline;
processmatchinfooffline = &storeoffline;
} else
{
processmatch = showmatch;
showmatchinfo.encseq = encseq;
showmatchinfo.characters = getencseqAlphabetcharacters(encseq);
showmatchinfo.wildcardshow = getencseqAlphabetwildcardshow(encseq);
showmatchinfo.showalignment = idxlocalioptions->showalignment;
processmatchinfoonline = processmatchinfooffline = &showmatchinfo;
}
if (idxlocalioptions->doonline || idxlocalioptions->docompare)
{
swdpresource = newSWdpresource(idxlocalioptions->matchscore,
idxlocalioptions->mismatchscore,
idxlocalioptions->gapextend,
idxlocalioptions->threshold,
idxlocalioptions->showalignment,
processmatch,
processmatchinfoonline);
}
dfst = locali_AbstractDfstransformer();
if (!idxlocalioptions->doonline || idxlocalioptions->docompare)
{
gt_assert(genericindex != NULL);
limdfsresources = newLimdfsresources(genericindex,
true,
0,
0, /* maxpathlength */
true, /* keepexpandedonstack */
processmatch,
processmatchinfooffline,
NULL, /* processresult */
NULL, /* processresult info */
dfst);
}
seqit = gt_seqiterator_new(idxlocalioptions->queryfiles, err);
if (!seqit)
haserr = true;
if (!haserr)
{
gt_seqiterator_set_symbolmap(seqit, getencseqAlphabetsymbolmap(encseq));
for (showmatchinfo.queryunit = 0; /* Nothing */;
showmatchinfo.queryunit++)
{
retval = gt_seqiterator_next(seqit,
&query,
&querylen,
&desc,
err);
if (retval < 0)
{
haserr = true;
break;
}
if (retval == 0)
{
break;
}
printf("process sequence " Formatuint64_t " of length %lu\n",
PRINTuint64_tcast(showmatchinfo.queryunit),querylen);
if (idxlocalioptions->doonline || idxlocalioptions->docompare)
{
multiapplysmithwaterman(swdpresource,encseq,query,querylen);
}
if (!idxlocalioptions->doonline || idxlocalioptions->docompare)
{
indexbasedlocali(limdfsresources,
idxlocalioptions->matchscore,
idxlocalioptions->mismatchscore,
idxlocalioptions->gapstart,
idxlocalioptions->gapextend,
idxlocalioptions->threshold,
query,
querylen,
dfst);
}
if (idxlocalioptions->docompare)
{
checkandresetstorematch(showmatchinfo.queryunit,
&storeonline,&storeoffline);
}
gt_free(desc);
}
if (limdfsresources != NULL)
{
freeLimdfsresources(&limdfsresources,dfst);
}
if (swdpresource != NULL)
{
freeSWdpresource(swdpresource);
swdpresource = NULL;
}
gt_seqiterator_delete(seqit);
}
if (idxlocalioptions->docompare)
{
freestorematch(&storeonline);
freestorematch(&storeoffline);
}
}
if (genericindex == NULL)
{
gt_assert(encseq != NULL);
encodedsequence_free((Encodedsequence **) &encseq);
} else
{
genericindex_delete(genericindex);
}
freeverboseinfo(&verboseinfo);
return haserr ? -1 : 0;
}
