static int inputsuffixarray(bool map,
Suffixarray *suffixarray,
unsigned int demand,
const GtStr *indexname,
Verboseinfo *verboseinfo,
GtError *err)
{
bool haserr = false;
Seqpos totallength = 0;
gt_error_check(err);
initsuffixarray(suffixarray);
suffixarray->encseq = mapencodedsequence(true,
indexname,
(demand & SARR_ESQTAB) ? true
: false,
(demand & SARR_DESTAB) ? true
: false,
(demand & SARR_SDSTAB) ? true
: false,
(demand & SARR_SSPTAB) ? true
: false,
verboseinfo,
err);
if (suffixarray->encseq == NULL)
{
haserr = true;
} else
{
totallength = getencseqtotallength(suffixarray->encseq);
}
if (!haserr)
{
haserr = scanprjfileuintkeys(suffixarray,indexname,verboseinfo,err);
}
if (!haserr && (demand & SARR_SUFTAB))
{
if (map)
{
suffixarray->suftab = genericmaptable(indexname,
SUFTABSUFFIX,
(unsigned long) (totallength+1),
sizeof (Seqpos),
err);
if (suffixarray->suftab == NULL)
{
haserr = true;
}
} else
{
INITBufferedfile(indexname,&suffixarray->suftabstream,Seqpos,
SUFTABSUFFIX);
}
if (!haserr && !suffixarray->longest.defined)
{
gt_error_set(err,"longest not defined");
haserr = true;
}
}
if (!haserr && (demand & SARR_LCPTAB))
{
if (map)
{
suffixarray->lcptab = genericmaptable(indexname,
LCPTABSUFFIX,
(unsigned long) (totallength+1),
sizeof (GtUchar),
err);
if (suffixarray->lcptab == NULL)
{
haserr = true;
}
} else
{
INITBufferedfile(indexname,&suffixarray->lcptabstream,GtUchar,
LCPTABSUFFIX);
if (!haserr &&
fseek(suffixarray->lcptabstream.fp,(long) sizeof (GtUchar),SEEK_SET))
{
gt_error_set(err,"fseek(esastream) failed: %s",strerror(errno));
haserr = true;
}
}
if (!haserr && !suffixarray->numoflargelcpvalues.defined)
{
gt_error_set(err,"numoflargelcpvalues not defined");
haserr = true;
}
if (!haserr && suffixarray->numoflargelcpvalues.valueseqpos > 0)
{
if (map)
{
suffixarray->llvtab
= genericmaptable(indexname,
LARGELCPTABSUFFIX,
(unsigned long) suffixarray->numoflargelcpvalues.
valueseqpos,
sizeof (Largelcpvalue),
err);
if (suffixarray->llvtab == NULL)
{
haserr = true;
}
} else
{
INITBufferedfile(indexname,&suffixarray->llvtabstream,Largelcpvalue,
LARGELCPTABSUFFIX);
}
}
}
if (!haserr && (demand & SARR_BWTTAB))
{
if (map)
{
suffixarray->bwttab = genericmaptable(indexname,
BWTTABSUFFIX,
(unsigned long) (totallength+1),
sizeof (GtUchar),
err);
if (suffixarray->bwttab == NULL)
{
haserr = true;
}
} else
{
INITBufferedfile(indexname,&suffixarray->bwttabstream,GtUchar,
BWTTABSUFFIX);
}
}
if (!haserr && (demand & SARR_BCKTAB))
{
if (map)
{
suffixarray->bcktab = mapbcktab(indexname,
getencseqAlphabetnumofchars(suffixarray->
encseq),
suffixarray->prefixlength,
err);
if (suffixarray->bcktab == NULL)
{
haserr = true;
}
} else
{
gt_error_set(err,"cannot stream bcktab");
haserr = true;
}
}
if (haserr)
{
freesuffixarray(suffixarray);
}
return haserr ? -1 : 0;
}
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;
}
