int gt_callenumselfmatches(const char *indexname,
GtReadmode queryreadmode,
unsigned int userdefinedleastlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtLogger *logger,
GtError *err)
{
Suffixarray suffixarray;
bool haserr = false;
gt_assert(queryreadmode != GT_READMODE_FORWARD);
if (gt_mapsuffixarray(&suffixarray,
SARR_ESQTAB | SARR_SUFTAB | SARR_SSPTAB,
indexname,
logger,
err) != 0)
{
haserr = true;
} else
{
unsigned long seqnum, numofsequences, seqlength, seqstartpos;
GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
GtQueryrep queryrep;
numofsequences = gt_encseq_num_of_sequences(suffixarray.encseq);
queryrep.sequence = NULL;
queryrep.reversecopy = false;
queryrep.encseq = suffixarray.encseq;
queryrep.readmode = queryreadmode;
for (seqnum = 0; seqnum < numofsequences; seqnum++)
{
seqstartpos = gt_encseq_seqstartpos(suffixarray.encseq, seqnum);
seqlength = gt_encseq_seqlength(suffixarray.encseq, seqnum);
if (seqlength >= (unsigned long) userdefinedleastlength)
{
queryrep.startpos = seqstartpos;
queryrep.length = seqlength;
if (gt_querysubstringmatch(true,
&suffixarray,
(uint64_t) seqnum,
&queryrep,
(unsigned long) userdefinedleastlength,
processquerymatch,
processquerymatchinfo,
querymatchspaceptr,
err) != 0)
{
haserr = true;
break;
}
}
}
gt_querymatch_delete(querymatchspaceptr);
}
gt_freesuffixarray(&suffixarray);
return haserr ? -1 : 0;
}
static int gt_constructsarrandrunmmsearch(
const GtEncseq *dbencseq,
GtReadmode readmode,
unsigned int prefixlength,
unsigned int numofparts,
GtUword maximumspace,
const GtUchar *query,
GtUword querylen,
unsigned int minlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtTimer *sfxprogress,
bool withprogressbar,
GtLogger *logger,
GtError *err)
{
bool haserr = false;
Sfxiterator *sfi;
Sfxstrategy sfxstrategy;
defaultsfxstrategy(&sfxstrategy,
gt_encseq_bitwise_cmp_ok(dbencseq) ? false : true);
sfxstrategy.outsuftabonfile = false;
sfi = gt_Sfxiterator_new(dbencseq,
readmode,
prefixlength,
numofparts,
maximumspace,
&sfxstrategy, /* sfxstrategy */
sfxprogress,
withprogressbar,
logger, /* logger */
err);
if (sfi == NULL)
{
haserr = true;
} else
{
const GtSuffixsortspace *suffixsortspace;
GtUword numberofsuffixes;
GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
GtQueryrepresentation queryrep;
queryrep.sequence = query;
queryrep.encseq = NULL;
queryrep.readmode = GT_READMODE_FORWARD;
queryrep.startpos = 0;
queryrep.seqlen = querylen;
while (true)
{
suffixsortspace = gt_Sfxiterator_next(&numberofsuffixes,NULL,sfi);
if (suffixsortspace == NULL)
{
break;
}
gt_querysubstringmatch(false,
dbencseq,
(const ESASuffixptr *)
gt_suffixsortspace_ulong_get(suffixsortspace),
readmode,
numberofsuffixes,
0,
&queryrep,
(GtUword) minlength,
processquerymatch,
processquerymatchinfo,
querymatchspaceptr);
}
gt_querymatch_delete(querymatchspaceptr);
}
if (gt_Sfxiterator_delete(sfi,err) != 0)
{
haserr = true;
}
return haserr ? -1 : 0;
}
static int gt_repfind_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments, GtError *err)
{
bool haserr = false;
Maxpairsoptions *arguments = tool_arguments;
GtLogger *logger = NULL;
GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
GtXdropmatchinfo xdropmatchinfo;
gt_error_check(err);
xdropmatchinfo.querymatchspaceptr = querymatchspaceptr;
xdropmatchinfo.useq = gt_seqabstract_new_empty();
xdropmatchinfo.vseq = gt_seqabstract_new_empty();
xdropmatchinfo.arbitscores.mat = 2;
xdropmatchinfo.arbitscores.mis = -2;
xdropmatchinfo.arbitscores.ins = -3;
xdropmatchinfo.arbitscores.del = -3;
xdropmatchinfo.frontresource = gt_frontresource_new(100UL);
xdropmatchinfo.res = gt_xdrop_resources_new(&xdropmatchinfo.arbitscores);
xdropmatchinfo.belowscore = 5L;
logger = gt_logger_new(arguments->beverbose, GT_LOGGER_DEFLT_PREFIX, stdout);
if (parsed_args < argc)
{
gt_error_set(err,"superfluous arguments: \"%s\"",argv[argc-1]);
haserr = true;
}
if (!haserr)
{
if (gt_str_array_size(arguments->queryfiles) == 0)
{
if (arguments->samples == 0)
{
if (arguments->forward)
{
GtProcessmaxpairs processmaxpairs;
void *processmaxpairsdata;
if (arguments->searchspm)
{
processmaxpairs = gt_simplesuffixprefixmatchoutput;
processmaxpairsdata = NULL;
} else
{
if (arguments->extendseed)
{
processmaxpairs = gt_simplexdropselfmatchoutput;
processmaxpairsdata = (void *) &xdropmatchinfo;
} else
{
processmaxpairs = gt_simpleexactselfmatchoutput;
processmaxpairsdata = (void *) querymatchspaceptr;
}
}
if (gt_callenummaxpairs(gt_str_get(arguments->indexname),
arguments->userdefinedleastlength,
arguments->scanfile,
processmaxpairs,
processmaxpairsdata,
logger,
err) != 0)
{
haserr = true;
}
}
if (!haserr && arguments->reverse)
{
if (gt_callenumselfmatches(gt_str_get(arguments->indexname),
GT_READMODE_REVERSE,
arguments->userdefinedleastlength,
/*arguments->extendseed
? gt_processxdropquerymatches
:*/ gt_querymatch_output,
/*arguments->extendseed
? (void *) &xdropmatchinfo
:*/ NULL,
logger,
err) != 0)
{
haserr = true;
}
}
} else
{
if (gt_testmaxpairs(gt_str_get(arguments->indexname),
arguments->samples,
arguments->userdefinedleastlength,
(GtUword)
(100 * arguments->userdefinedleastlength),
logger,
err) != 0)
{
haserr = true;
}
}
} else
{
if (gt_callenumquerymatches(gt_str_get(arguments->indexname),
arguments->queryfiles,
false,
true,
false,
arguments->userdefinedleastlength,
NULL,
arguments->extendseed
? gt_processxdropquerymatches
: gt_querymatch_output,
arguments->extendseed
? (void *) &xdropmatchinfo
: NULL,
logger,
err) != 0)
{
haserr = true;
}
}
}
gt_querymatch_delete(querymatchspaceptr);
gt_seqabstract_delete(xdropmatchinfo.useq);
gt_seqabstract_delete(xdropmatchinfo.vseq);
gt_xdrop_resources_delete(xdropmatchinfo.res);
gt_frontresource_delete(xdropmatchinfo.frontresource);
gt_logger_delete(logger);
return haserr ? -1 : 0;
}
static int gt_callenumquerymatches_withindex(
GtQuerysubstringmatchfunc findquerymatches,
const Suffixarray *suffixarray,
const GtStrArray *queryfiles,
bool forwardstrand,
bool reversestrand,
unsigned int userdefinedleastlength,
GtProcessquerybeforematching
processquerybeforematching,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtError *err)
{
GtSeqIterator *seqit;
bool haserr = false;
seqit = gt_seq_iterator_sequence_buffer_new(queryfiles, err);
if (seqit == NULL)
{
haserr = true;
} else
{
GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
const GtUchar *query;
unsigned long querylen;
int retval;
uint64_t queryunitnum;
GtUchar *queryreverse = NULL;
unsigned long queryreverse_length = 0;
char *desc = NULL;
int mode;
gt_seq_iterator_set_symbolmap(seqit,
gt_alphabet_symbolmap(gt_encseq_alphabet(
suffixarray->encseq)));
for (queryunitnum = 0; /* Nothing */; queryunitnum++)
{
retval = gt_seq_iterator_next(seqit, &query, &querylen, &desc, err);
if (retval < 0)
{
haserr = true;
break;
}
if (retval == 0)
{
break;
}
if (querylen >= (unsigned long) userdefinedleastlength)
{
GtQueryrep queryrep;
queryrep.encseq = NULL;
queryrep.readmode = GT_READMODE_FORWARD;
queryrep.startpos = 0;
queryrep.length = querylen;
for (mode = 0; mode <= 1; mode++)
{
if (mode == 0 && forwardstrand)
{
queryrep.sequence = query;
queryrep.reversecopy = false;
if (processquerybeforematching != NULL)
{
processquerybeforematching(processquerymatchinfo,desc,query,
querylen,true);
}
} else
{
if (mode == 1 && reversestrand)
{
if (querylen > queryreverse_length)
{
queryreverse = gt_realloc(queryreverse,
sizeof (*queryreverse) * querylen);
queryreverse_length = querylen;
}
gt_copy_reversecomplement(queryreverse,query,querylen);
queryrep.sequence = queryreverse;
queryrep.reversecopy = true;
if (processquerybeforematching != NULL)
{
processquerybeforematching(processquerymatchinfo,desc,
queryreverse,querylen,false);
}
} else
{
queryrep.sequence = NULL;
queryrep.reversecopy = false;
}
}
if (queryrep.sequence != NULL)
{
int ret = findquerymatches(false,
suffixarray,
queryunitnum,
&queryrep,
(unsigned long) userdefinedleastlength,
processquerymatch,
processquerymatchinfo,
querymatchspaceptr,
err);
if (ret != 0)
{
haserr = true;
break;
}
}
}
}
}
gt_seq_iterator_delete(seqit);
gt_free(queryreverse);
gt_querymatch_delete(querymatchspaceptr);
}
return haserr ? -1 : 0;
}