int gt_querysubstringmatchiterator_next(GtQuerysubstringmatchiterator *qsmi,
GtError *err)
{
gt_assert(qsmi != NULL);
while (true)
{
if (qsmi->query_seqlen < qsmi->userdefinedleastlength)
{
if (qsmi->seqit != NULL)
{
int retval = gt_seq_iterator_next(qsmi->seqit,
&qsmi->query_for_seqit,
&qsmi->query_seqlen,
&qsmi->desc,
err);
if (retval < 0)
{
return -1; /* error */
}
if (retval == 0)
{
return 1; /* no more sequences */
}
gt_assert(qsmi->query_seqlen > 0 && qsmi->query_for_seqit != NULL);
qsmi->queryrep.sequence = qsmi->query_for_seqit;
} else
{
if (qsmi->queryunitnum == qsmi->query_encseq_numofsequences)
{
return 1;
}
qsmi->queryrep.startpos = gt_encseq_seqstartpos(qsmi->queryrep.encseq,
qsmi->queryunitnum);
qsmi->query_seqlen = gt_encseq_seqlength(qsmi->queryrep.encseq,
qsmi->queryunitnum);
}
gt_assert(qsmi->query_seqlen > 0);
qsmi->queryrep.seqlen = qsmi->query_seqlen;
qsmi->querysubstring.currentoffset = 0;
}
if (qsmi->query_seqlen >= qsmi->userdefinedleastlength)
{
if (!qsmi->mmsi_defined)
{
gt_mmsearchiterator_reinit(qsmi->mmsi,
qsmi->dbencseq,
qsmi->suftabpart,
0, /* l */
qsmi->numberofsuffixes - 1, /* r */
0, /* offset */
qsmi->db_readmode,
&qsmi->querysubstring,
qsmi->userdefinedleastlength);
qsmi->mmsi_defined = true;
} else
{
if (gt_mmsearchiterator_next(&qsmi->dbstart,qsmi->mmsi))
{
GtUword extend;
if (gt_mmsearch_isleftmaximal(qsmi->dbencseq,
qsmi->db_readmode,
qsmi->dbstart,
&qsmi->querysubstring))
{
extend = gt_mmsearch_extendright(qsmi->dbencseq,
qsmi->mmsi->esr,
qsmi->db_readmode,
qsmi->totallength,
qsmi->dbstart +
qsmi->userdefinedleastlength,
&qsmi->querysubstring,
qsmi->userdefinedleastlength);
qsmi->matchlength = qsmi->userdefinedleastlength + extend;
return 0;
}
} else
{
qsmi->mmsi_defined = false;
if (qsmi->querysubstring.currentoffset +
qsmi->userdefinedleastlength < qsmi->query_seqlen)
{
qsmi->querysubstring.currentoffset++;
} else
{
qsmi->query_seqlen = 0;
qsmi->queryunitnum++;
}
}
}
} else
{
qsmi->query_seqlen = 0;
qsmi->queryunitnum++;
}
}
}
extern int
gt_packedindex_chk_search(int argc, const char *argv[], GtError *err)
{
struct chkSearchOptions params;
Suffixarray suffixarray;
Enumpatterniterator *epi = NULL;
bool saIsLoaded = false;
BWTSeq *bwtSeq = NULL;
GtStr *inputProject = NULL;
int parsedArgs;
bool had_err = false;
BWTSeqExactMatchesIterator EMIter;
bool EMIterInitialized = false;
GtLogger *logger = NULL;
inputProject = gt_str_new();
do {
gt_error_check(err);
{
bool exitNow = false;
switch (parseChkBWTOptions(&parsedArgs, argc, argv, ¶ms,
inputProject, err))
{
case GT_OPTION_PARSER_OK:
break;
case GT_OPTION_PARSER_ERROR:
had_err = true;
exitNow = true;
break;
case GT_OPTION_PARSER_REQUESTS_EXIT:
exitNow = true;
break;
}
if (exitNow)
break;
}
gt_str_set(inputProject, argv[parsedArgs]);
logger = gt_logger_new(params.verboseOutput,
GT_LOGGER_DEFLT_PREFIX, stdout);
bwtSeq = gt_availBWTSeq(¶ms.idx.final, logger, err);
if ((had_err = bwtSeq == NULL))
break;
{
enum verifyBWTSeqErrCode retval =
gt_BWTSeqVerifyIntegrity(bwtSeq, gt_str_get(inputProject), params.flags,
params.progressInterval, stderr, logger, err);
if ((had_err = (retval != VERIFY_BWTSEQ_NO_ERROR)))
{
fprintf(stderr, "index integrity check failed: %s\n",
gt_error_get(err));
gt_error_set(err, "aborted because of index integrity check fail");
break;
}
}
if (BWTSeqHasLocateInformation(bwtSeq))
{
if ((had_err = !gt_initEmptyEMIterator(&EMIter, bwtSeq)))
{
gt_error_set(err, "Cannot create matches iterator for sequence index.");
break;
}
EMIterInitialized = true;
}
{
unsigned long totalLen, dbstart;
unsigned long trial, patternLen;
if ((had_err =
gt_mapsuffixarray(&suffixarray, SARR_SUFTAB | SARR_ESQTAB,
gt_str_get(inputProject), NULL, err) != 0))
{
gt_error_set(err, "Can't load suffix array project with"
" demand for encoded sequence and suffix table files\n");
break;
}
totalLen = gt_encseq_total_length(suffixarray.encseq);
saIsLoaded = true;
if ((had_err = (params.minPatLen >= 0L && params.maxPatLen >= 0L
&& params.minPatLen > params.maxPatLen)))
{
gt_error_set(err, "Invalid pattern lengths selected: min=%ld, max=%ld;"
" min <= max is required.", params.minPatLen,
params.maxPatLen);
break;
}
if (params.minPatLen < 0 || params.maxPatLen < 0)
{
unsigned int numofchars
= gt_alphabet_num_of_chars(
gt_encseq_alphabet(suffixarray.encseq));
if (params.minPatLen < 0)
params.minPatLen
= gt_recommendedprefixlength(numofchars,
totalLen,
GT_RECOMMENDED_MULTIPLIER_DEFAULT,
true);
if (params.maxPatLen < 0)
params.maxPatLen =
MAX(params.minPatLen,
125 * gt_recommendedprefixlength(numofchars,totalLen,
GT_RECOMMENDED_MULTIPLIER_DEFAULT,
true)/100);
else
params.maxPatLen = MAX(params.maxPatLen, params.minPatLen);
}
fprintf(stderr, "Using patterns of lengths %lu to %lu\n",
params.minPatLen, params.maxPatLen);
if ((had_err = totalLen + 1 != BWTSeqLength(bwtSeq)))
{
gt_error_set(err, "base suffix array and index have diferrent lengths!"
"%lu vs. %lu", totalLen + 1,
BWTSeqLength(bwtSeq));
break;
}
if ((had_err =
(epi = gt_newenumpatterniterator(params.minPatLen, params.maxPatLen,
suffixarray.encseq,
err)) == NULL))
{
fputs("Creation of pattern iterator failed!\n", stderr);
break;
}
for (trial = 0; !had_err && trial < params.numOfSamples; ++trial)
{
const GtUchar *pptr = gt_nextEnumpatterniterator(&patternLen, epi);
GtMMsearchiterator *mmsi =
gt_mmsearchiterator_new_complete_olain(suffixarray.encseq,
suffixarray.suftab,
0, /* leftbound */
totalLen, /* rightbound */
0, /* offset */
suffixarray.readmode,
pptr,
patternLen);
if (BWTSeqHasLocateInformation(bwtSeq))
{
if ((had_err = !gt_reinitEMIterator(&EMIter, bwtSeq, pptr, patternLen,
false)))
{
fputs("Internal error: failed to reinitialize pattern match"
" iterator", stderr);
abort();
}
gt_assert(gt_EMINumMatchesTotal(&EMIter) ==
gt_BWTSeqMatchCount(bwtSeq, pptr, patternLen,
false));
gt_assert(gt_EMINumMatchesTotal(&EMIter)
== gt_mmsearchiterator_count(mmsi));
while (gt_mmsearchiterator_next(&dbstart,mmsi))
{
unsigned long matchPos = 0;
bool match = EMIGetNextMatch(&EMIter, &matchPos, bwtSeq);
if ((had_err = !match))
{
gt_error_set(err,
"matches of packedindex expired before mmsearch!");
break;
}
if ((had_err = matchPos != dbstart))
{
gt_error_set(err, "packedindex match doesn't equal mmsearch "
"match result!\n%lu vs. %lu\n",
matchPos, dbstart);
}
}
if (!had_err)
{
unsigned long matchPos;
bool trailingMatch = EMIGetNextMatch(&EMIter, &matchPos, bwtSeq);
if ((had_err = trailingMatch))
{
gt_error_set(err, "matches of mmsearch expired before fmindex!");
break;
}
}
}
else
{
unsigned long numFMIMatches = gt_BWTSeqMatchCount(bwtSeq, pptr,
patternLen,
false),
numMMSearchMatches = gt_mmsearchiterator_count(mmsi);
if ((had_err = numFMIMatches != numMMSearchMatches))
{
gt_error_set(err, "Number of matches not equal for suffix array ("
"%lu) and fmindex (%lu).\n",
numFMIMatches, numMMSearchMatches);
}
}
gt_mmsearchiterator_delete(mmsi);
mmsi = NULL;
if (params.progressInterval && !((trial + 1) % params.progressInterval))
putc('.', stderr);
}
if (params.progressInterval)
putc('\n', stderr);
fprintf(stderr, "Finished %lu of %lu matchings successfully.\n",
trial, params.numOfSamples);
}
} while (0);
if (EMIterInitialized) gt_destructEMIterator(&EMIter);
if (saIsLoaded) gt_freesuffixarray(&suffixarray);
gt_freeEnumpatterniterator(epi);
if (bwtSeq) gt_deleteBWTSeq(bwtSeq);
if (logger) gt_logger_delete(logger);
if (inputProject) gt_str_delete(inputProject);
return had_err?-1:0;
}
static void gt_querysubstringmatch(bool selfmatch,
const GtEncseq *dbencseq,
const ESASuffixptr *suftabpart,
GtReadmode readmode,
GtUword numberofsuffixes,
uint64_t queryunitnum,
GtQueryrepresentation *queryrep,
GtUword minmatchlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtQuerymatch *querymatchspaceptr)
{
GtMMsearchiterator *mmsi;
GtUword totallength, localqueryoffset = 0;
uint64_t localqueryunitnum = queryunitnum;
GtQuerysubstring querysubstring;
gt_assert(numberofsuffixes > 0);
totallength = gt_encseq_total_length(dbencseq);
querysubstring.queryrep = queryrep;
for (querysubstring.currentoffset = 0;
querysubstring.currentoffset <= queryrep->seqlen - minmatchlength;
querysubstring.currentoffset++)
{
GtUword dbstart;
mmsi = gt_mmsearchiterator_new(dbencseq,
suftabpart,
0, /* leftbound */
numberofsuffixes - 1, /* rightbound */
0, /* offset */
readmode,
&querysubstring,
minmatchlength);
while (gt_mmsearchiterator_next(&dbstart,mmsi))
{
if (gt_mmsearch_isleftmaximal(dbencseq,
readmode,
dbstart,
&querysubstring))
{
GtUword dbseqnum, dbseqstartpos, dbseqlen, extend;
extend = gt_mmsearch_extendright(dbencseq,
mmsi->esr,
readmode,
totallength,
dbstart + minmatchlength,
&querysubstring,
minmatchlength);
if (gt_encseq_has_multiseq_support(dbencseq))
{
dbseqnum = gt_encseq_seqnum(dbencseq,dbstart);
dbseqstartpos = gt_encseq_seqstartpos(dbencseq,dbseqnum);
dbseqlen = gt_encseq_seqlength(dbencseq,dbseqnum);
} else
{
dbseqnum = dbseqstartpos = dbseqlen = 0;
}
gt_querymatch_init(querymatchspaceptr,
minmatchlength + extend,
dbstart,
dbseqnum,
dbstart - dbseqstartpos,
dbseqlen,
0, /* score */
0, /* edist */
selfmatch,
localqueryunitnum,
minmatchlength + extend,
localqueryoffset,
queryrep->seqlen);
processquerymatch(processquerymatchinfo,querymatchspaceptr);
}
}
gt_mmsearchiterator_delete(mmsi);
mmsi = NULL;
if (gt_mmsearch_accessquery(queryrep,querysubstring.currentoffset)
== (GtUchar) SEPARATOR)
{
localqueryunitnum++;
localqueryoffset = 0;
} else
{
localqueryoffset++;
}
}
}
static int gt_querysubstringmatch_generic(
bool selfmatch,
const GtEncseq *dbencseq,
const ESASuffixptr *suftabpart,
GtReadmode readmode,
unsigned long numberofsuffixes,
uint64_t queryunitnum,
const GtQueryrep *queryrep,
unsigned long minmatchlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtQuerymatch *querymatchspaceptr,
GtError *err)
{
GtMMsearchiterator *mmsi;
unsigned long totallength, localqueryoffset = 0;
uint64_t localqueryunitnum = queryunitnum;
GtQuerysubstring querysubstring;
bool haserr = false;
gt_assert(numberofsuffixes > 0);
totallength = gt_encseq_total_length(dbencseq);
querysubstring.queryrep = queryrep;
for (querysubstring.offset = 0;
querysubstring.offset <= queryrep->length - minmatchlength;
querysubstring.offset++)
{
unsigned long dbstart;
mmsi = gt_mmsearchiterator_new_generic(dbencseq,
suftabpart,
0, /* leftbound */
numberofsuffixes-1, /* rightbound */
0, /* offset */
readmode,
&querysubstring,
minmatchlength);
while (!haserr && gt_mmsearchiterator_next(&dbstart,mmsi))
{
if (gt_mmsearch_isleftmaximal(dbencseq,
readmode,
dbstart,
&querysubstring))
{
unsigned long extend = gt_mmsearch_extendright(dbencseq,
mmsi->esr,
readmode,
totallength,
dbstart + minmatchlength,
&querysubstring,
minmatchlength);
gt_querymatch_fill(querymatchspaceptr,
minmatchlength + extend,
dbstart,
queryrep->readmode,
queryrep->reversecopy,
0, /* score */
0, /* edist */
selfmatch,
localqueryunitnum,
minmatchlength + extend,
localqueryoffset);
if (processquerymatch(processquerymatchinfo,
dbencseq,
querymatchspaceptr,
queryrep->sequence,
queryrep->length,
err) != 0)
{
haserr = true;
}
}
}
gt_mmsearchiterator_delete(mmsi);
mmsi = NULL;
if (!haserr)
{
if (gt_mmsearch_accessquery(queryrep,querysubstring.offset)
== (GtUchar) SEPARATOR)
{
localqueryunitnum++;
localqueryoffset = 0;
} else
{
localqueryoffset++;
}
}
}
return haserr ? -1 : 0;
}