static int runmkfmindex(Mkfmcallinfo *mkfmcallinfo,GtLogger *logger,
GtError *err)
{
Fmindex fm;
unsigned int log2bsize,
log2markdist;
bool haserr = false;
GtSpecialcharinfo specialcharinfo;
gt_error_check(err);
GT_INITARRAY(&fm.specpos, GtPairBwtidx);
fm.bfreq = NULL;
fm.superbfreq = NULL;
fm.tfreq = NULL;
fm.markpostable = NULL;
fm.boundarray = NULL;
fm.suffixlength = 0;
if (levedescl2levelnum(gt_str_get(mkfmcallinfo->leveldesc),
&log2bsize,
&log2markdist) != 0)
{
gt_error_set(err,"undefined level \"%s\"",
gt_str_get(mkfmcallinfo->leveldesc));
haserr = true;
}
if (!haserr && gt_sufbwt2fmindex(&fm,
&specialcharinfo,
log2bsize,
log2markdist,
gt_str_get(mkfmcallinfo->outfmindex),
mkfmcallinfo->indexnametab,
mkfmcallinfo->noindexpos ? false : true,
logger,
err) != 0)
{
haserr = true;
}
if (!haserr && gt_saveFmindex(gt_str_get(mkfmcallinfo->outfmindex),
&fm,
&specialcharinfo,
mkfmcallinfo->noindexpos ? false : true,
err) < 0)
{
haserr = true;
}
freeconstructedfmindex(&fm);
return haserr ? -1 : 0;
}
GtBareEncseq *gt_bare_encseq_new(GtUchar *sequence,GtUword len,
GtUword numofchars)
{
GtBareEncseq *bare_encseq = gt_malloc(sizeof *bare_encseq);
const GtUchar *readptr;
GtBareSpecialrange *srptr = NULL;
GtUword lastspecialrange_length = 0;
bare_encseq->specialcharacters = 0;
bare_encseq->numofchars = numofchars;
bare_encseq->charcount = gt_calloc((size_t) bare_encseq->numofchars,
sizeof *bare_encseq->charcount);
GT_INITARRAY(&bare_encseq->specialranges,GtBareSpecialrange);
for (readptr = sequence; readptr < sequence + len; readptr++)
{
GtUchar cc = *readptr;
if (ISSPECIAL(cc))
{
if (lastspecialrange_length == 0)
{
GT_GETNEXTFREEINARRAY(srptr,&bare_encseq->specialranges,
GtBareSpecialrange,128UL);
srptr->start = (GtUword) (readptr - sequence);
}
lastspecialrange_length++;
bare_encseq->specialcharacters++;
} else
{
gt_assert((GtUword) cc < bare_encseq->numofchars);
bare_encseq->charcount[(int) cc]++;
if (lastspecialrange_length > 0)
{
gt_assert(srptr != NULL);
srptr->length = lastspecialrange_length;
}
lastspecialrange_length = 0;
}
}
if (lastspecialrange_length > 0)
{
gt_assert(srptr != NULL);
srptr->length = lastspecialrange_length;
}
bare_encseq->sequence = sequence;
bare_encseq->totallength = len;
return bare_encseq;
}
GtSeqIterator* gt_seq_iterator_sequence_buffer_new_with_buffer(
GtSequenceBuffer *buffer)
{
GtSeqIterator *si;
GtSeqIteratorSequenceBuffer *seqit;
si = gt_seq_iterator_create(gt_seq_iterator_sequence_buffer_class());
seqit = gt_seq_iterator_sequence_buffer_cast(si);
GT_INITARRAY(&seqit->sequencebuffer, GtUchar);
seqit->descptr = gt_desc_buffer_new();
seqit->fb = gt_sequence_buffer_ref(buffer);
gt_sequence_buffer_set_desc_buffer(seqit->fb, seqit->descptr);
seqit->exhausted = false;
seqit->unitnum = 0;
seqit->withsequence = true;
seqit->currentread = 0;
seqit->maxread = 0;
return si;
}
static void gt_kmer_database_add_to_hash(GtHashmap *hash, GtCodetype kmercode,
GtUword position)
{
GtArrayGtUword *arr =
(GtArrayGtUword *) gt_hashmap_get(hash, (void *) kmercode);
if (arr == NULL) {
arr = gt_malloc(sizeof (*arr));
GT_INITARRAY(arr, GtUword);
gt_hashmap_add(hash, (void *) kmercode, (void *) arr);
}
if (arr->allocatedGtUword == 0)
GT_STOREINARRAY(arr, GtUword,
(GtUword) 20,
position);
else
GT_STOREINARRAY(arr, GtUword,
arr->allocatedGtUword * 0.1,
position);
}
int gt_verifymappedstr(const GtEncseq *encseq,
unsigned int prefixlength,
GtError *err)
{
unsigned int numofchars;
GtArrayGtCodetype codeliststream;
bool haserr = false;
gt_error_check(err);
numofchars = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));
GT_INITARRAY(&codeliststream,GtCodetype);
if (getfastastreamkmers(gt_encseq_filenames(encseq),
numofchars,
prefixlength,
gt_alphabet_symbolmap(
gt_encseq_alphabet(encseq)),
false,
&codeliststream,
err) != 0)
{
haserr = true;
}
if (!haserr)
{
if (verifycodelists(encseq,
prefixlength,
numofchars,
&codeliststream,
err) != 0)
{
haserr = true;
}
}
GT_FREEARRAY(&codeliststream,GtCodetype);
return haserr ? -1 : 0;
}
/*read condenseq data structure from file*/
GtCondenseq *gt_condenseq_new_from_file(const char *indexname,
GtLogger *logger, GtError *err)
{
int had_err = 0;
FILE* fp;
GtEncseqLoader *esl;
GtEncseq *unique_es;
GtCondenseq *condenseq = NULL;
/*load unique_es*/
esl = gt_encseq_loader_new();
unique_es = gt_encseq_loader_load(esl, indexname, err);
if (!unique_es)
had_err = -1;
if (!had_err) {
gt_encseq_loader_delete(esl);
condenseq = condenseq_new_empty(gt_encseq_alphabet(unique_es));
condenseq->filename = gt_cstr_dup(indexname);
condenseq->unique_es = unique_es;
fp = gt_fa_fopen_with_suffix(indexname, GT_CONDENSEQ_FILE_SUFFIX,
"rb", err);
if (fp == NULL) {
had_err = -1;
}
else {
had_err = condenseq_io(condenseq, fp, gt_io_error_fread, err);
if (!had_err) {
GtUword i;
gt_assert(condenseq->uniques);
gt_assert(condenseq->links);
gt_fa_fclose(fp);
/*create link array for each unique entry*/
for (i = 0; i < condenseq->udb_nelems; i++) {
GT_INITARRAY(&(condenseq->uniques[i].links),uint32_t);
}
/* check for overflows */
if (condenseq->ldb_nelems > (GtUword) ((uint32_t) 0 - (uint32_t) 1)) {
gt_error_set(err, "Overflow, to many link-elements. Can't be stored");
had_err = -1;
}
/* iterate through link entrys and store ids in corresponding unique
entry array */
for (i = 0; !had_err && (GtUword) i < condenseq->ldb_nelems; i++) {
GtUword uid = condenseq->links[i].unique_id;
gt_assert(uid < condenseq->udb_nelems);
GT_STOREINARRAY(&(condenseq->uniques[uid].links),
uint32_t,
10,
(uint32_t) i);
}
}
}
}
if (!had_err) {
gt_assert(condenseq != NULL);
if (condenseq->id_len != GT_UNDEF_UWORD)
gt_logger_log(logger, "IDs const len: " GT_WU, condenseq->id_len);
else
gt_logger_log(logger, "using sdstab to access IDs");
}
if (had_err) {
gt_condenseq_delete(condenseq);
condenseq = NULL;
}
return (condenseq);
}
GtOutlcpinfo *gt_Outlcpinfo_new(const char *indexname,
unsigned int numofchars,
unsigned int prefixlength,
bool withdistribution,
bool swallow_tail_lcpvalues,
GtFinalProcessBucket final_process_bucket,
void *final_process_bucket_info,
GtError *err)
{
bool haserr = false;
GtOutlcpinfo *outlcpinfo;
outlcpinfo = gt_malloc(sizeof (*outlcpinfo));
outlcpinfo->sizeofinfo = sizeof (*outlcpinfo);
outlcpinfo->lcpsubtab.lcptabsum = 0.0;
outlcpinfo->swallow_tail_lcpvalues = swallow_tail_lcpvalues;
if (withdistribution)
{
outlcpinfo->lcpsubtab.distlcpvalues = gt_disc_distri_new();
} else
{
outlcpinfo->lcpsubtab.distlcpvalues = NULL;
}
if (indexname == NULL)
{
outlcpinfo->lcpsubtab.lcp2file = NULL;
if (final_process_bucket != NULL)
{
outlcpinfo->lcpsubtab.lcpprocess
= gt_malloc(sizeof (*outlcpinfo->lcpsubtab.lcpprocess));
outlcpinfo->lcpsubtab.lcpprocess->final_process_bucket
= final_process_bucket;
outlcpinfo->lcpsubtab.lcpprocess->final_process_bucket_info
= final_process_bucket_info;
} else
{
outlcpinfo->lcpsubtab.lcpprocess = NULL;
}
} else
{
outlcpinfo->lcpsubtab.lcpprocess = NULL;
outlcpinfo->lcpsubtab.lcp2file
= gt_malloc(sizeof (*outlcpinfo->lcpsubtab.lcp2file));
outlcpinfo->sizeofinfo += sizeof (*outlcpinfo->lcpsubtab.lcp2file);
outlcpinfo->lcpsubtab.lcp2file->countoutputlcpvalues = 0;
outlcpinfo->lcpsubtab.lcp2file->maxbranchdepth = 0;
outlcpinfo->lcpsubtab.lcp2file->totalnumoflargelcpvalues = 0;
outlcpinfo->lcpsubtab.lcp2file->reservoir = NULL;
outlcpinfo->lcpsubtab.lcp2file->sizereservoir = 0;
outlcpinfo->lcpsubtab.lcp2file->smalllcpvalues = NULL;
GT_INITARRAY(&outlcpinfo->lcpsubtab.lcp2file->largelcpvalues,
Largelcpvalue);
outlcpinfo->lcpsubtab.lcp2file->outfplcptab
= gt_fa_fopen_with_suffix(indexname,GT_LCPTABSUFFIX,"wb",err);
if (outlcpinfo->lcpsubtab.lcp2file->outfplcptab == NULL)
{
haserr = true;
}
if (!haserr)
{
outlcpinfo->lcpsubtab.lcp2file->outfpllvtab
= gt_fa_fopen_with_suffix(indexname,GT_LARGELCPTABSUFFIX,"wb",err);
if (outlcpinfo->lcpsubtab.lcp2file->outfpllvtab == NULL)
{
haserr = true;
}
}
}
outlcpinfo->numsuffixes2output = 0;
outlcpinfo->minchanged = 0;
if (!haserr && prefixlength > 0)
{
outlcpinfo->turnwheel = gt_turningwheel_new(prefixlength,numofchars);
outlcpinfo->sizeofinfo += gt_turningwheel_size();
} else
{
outlcpinfo->turnwheel = NULL;
}
#ifdef SKDEBUG
outlcpinfo->previoussuffix.startpos = 0;
#endif
outlcpinfo->previoussuffix.code = 0;
outlcpinfo->previoussuffix.prefixindex = 0;
outlcpinfo->previoussuffix.defined = false;
outlcpinfo->previousbucketwasempty = false;
outlcpinfo->lcpsubtab.tableoflcpvalues.bucketoflcpvalues = NULL;
outlcpinfo->lcpsubtab.tableoflcpvalues.numofentries = 0;
#ifndef NDEBUG
outlcpinfo->lcpsubtab.tableoflcpvalues.isset = NULL;
#endif
if (haserr)
{
gt_free(outlcpinfo);
return NULL;
}
return outlcpinfo;
}
Pckbuckettable *pckbuckettable_new(const void *voidbwtseq,
unsigned int numofchars,
Seqpos totallength,
unsigned int maxdepth)
{
GtArrayBoundsatdepth stack;
Boundsatdepth parent, child;
unsigned long rangesize, idx;
Seqpos *rangeOccs;
Pckbuckettable *pckbt;
Mbtab *tmpmbtab;
GT_INITARRAY(&stack,Boundsatdepth);
child.lowerbound = 0;
child.upperbound = totallength+1;
child.depth = 0;
child.code = (Codetype) 0;
GT_STOREINARRAY(&stack,Boundsatdepth,128,child);
rangeOccs = gt_malloc(sizeof(*rangeOccs) * GT_MULT2(numofchars));
tmpmbtab = gt_malloc(sizeof(*tmpmbtab) * numofchars);
pckbt = allocandinitpckbuckettable(numofchars,maxdepth,true);
while (stack.nextfreeBoundsatdepth > 0)
{
parent = stack.spaceBoundsatdepth[--stack.nextfreeBoundsatdepth];
gt_assert(parent.lowerbound < parent.upperbound);
rangesize = bwtrangesplitallwithoutspecial(tmpmbtab,
rangeOccs,
voidbwtseq,
parent.lowerbound,
parent.upperbound);
gt_assert(rangesize <= (unsigned long) numofchars);
for (idx = 0; idx < rangesize; idx++)
{
child.lowerbound = tmpmbtab[idx].lowerbound;
child.upperbound = tmpmbtab[idx].upperbound;
child.depth = parent.depth + 1;
gt_assert(child.depth <= maxdepth);
child.code = parent.code * numofchars + idx;
/*
printf("depth=%lu code=%lu: %lu %lu\n",
child.depth,child.code,(unsigned long) child.lowerbound,
(unsigned long) child.upperbound);
*/
storeBoundsatdepth(pckbt,&child);
if (child.depth < maxdepth)
{
if (child.lowerbound + 1 < child.upperbound)
{
GT_STOREINARRAY(&stack,Boundsatdepth,128,child);
} else
{
followleafedge(pckbt,voidbwtseq,&child);
}
}
}
}
GT_FREEARRAY(&stack,Boundsatdepth);
gt_free(rangeOccs);
gt_free(tmpmbtab);
printf("filled: %lu (%.2f)\n",pckbt->numofvalues,
(double) pckbt->numofvalues/pckbt->maxnumofvalues);
return pckbt;
}
int gt_mapspec_write(GtMapspecSetupFunc setup, FILE *fp,
void *data, GtUword expectedsize, GtError *err)
{
GtMapspecification *mapspecptr;
GtUword byteoffset = 0;
int had_err = 0;
GtUword totalpadunits = 0;
GtUword byteswritten;
GtMapspec *ms = gt_malloc(sizeof (GtMapspec));
gt_error_check(err);
GT_INITARRAY(&ms->mapspectable,GtMapspecification);
setup(ms, data, true);
gt_assert(ms->mapspectable.spaceGtMapspecification != NULL);
for (mapspecptr = ms->mapspectable.spaceGtMapspecification;
mapspecptr < ms->mapspectable.spaceGtMapspecification +
ms->mapspectable.nextfreeGtMapspecification;
mapspecptr++)
{
#ifdef SKDEBUG
printf("# %s",__func__);
showmapspec(mapspecptr);
printf(" at byteoffset "GT_WU"\n",byteoffset);
#endif
if (mapspecptr->numofunits > 0)
{
switch (mapspecptr->typespec)
{
case GtCharType:
WRITEACTIONWITHTYPE(char);
break;
case GtFilelengthvaluesType:
WRITEACTIONWITHTYPE(GtFilelengthvalues);
break;
case GtUcharType:
WRITEACTIONWITHTYPE(GtUchar);
break;
case Uint16Type:
WRITEACTIONWITHTYPE(uint16_t);
break;
case Uint32Type:
WRITEACTIONWITHTYPE(uint32_t);
break;
case GtUlongType:
WRITEACTIONWITHTYPE(GtUlong);
break;
case Uint64Type:
WRITEACTIONWITHTYPE(uint64_t);
break;
case GtBitsequenceType:
WRITEACTIONWITHTYPE(GtBitsequence);
break;
case GtUlongBoundType:
WRITEACTIONWITHTYPE(GtUlongBound);
break;
case GtPairBwtidxType:
WRITEACTIONWITHTYPE(GtPairBwtidx);
break;
case GtTwobitencodingType:
WRITEACTIONWITHTYPE(GtTwobitencoding);
break;
case GtSpecialcharinfoType:
WRITEACTIONWITHTYPE(GtSpecialcharinfo);
break;
case GtBitElemType:
WRITEACTIONWITHTYPE(BitElem);
break;
case GtUintType:
WRITEACTIONWITHTYPE(unsigned int);
break;
default:
gt_error_set(err, "no map specification for size " GT_WU,
(GtUword) mapspecptr->sizeofunit);
had_err = -1;
}
}
if (had_err)
{
break;
}
byteoffset = CALLCASTFUNC(uint64_t,unsigned_long,
(uint64_t) (byteoffset +
mapspecptr->sizeofunit *
mapspecptr->numofunits));
if (gt_mapspec_pad(fp,&byteswritten,byteoffset,err) != 0)
{
had_err = -1;
}
byteoffset += byteswritten;
totalpadunits += byteswritten;
}
if (!had_err)
{
if (expectedsize + totalpadunits != byteoffset)
{
gt_error_set(err, "expected file size is " GT_WU " bytes, "
"but file has " GT_WU " bytes",
expectedsize, byteoffset);
had_err = -1;
}
}
GT_FREEARRAY(&ms->mapspectable,GtMapspecification);
gt_free(ms);
return had_err;
}
int gt_mapspec_read(GtMapspecSetupFunc setup, void *data,
const char *filename, GtUword expectedsize,
void **mapped, GtError *err)
{
void *mapptr;
uint64_t expectedaccordingtomapspec;
GtUword byteoffset = 0;
size_t numofbytes;
GtMapspec *ms = gt_malloc(sizeof (GtMapspec));
GtMapspecification *mapspecptr;
int had_err = 0;
GtUword totalpadunits = 0;
gt_error_check(err);
GT_INITARRAY(&ms->mapspectable, GtMapspecification);
setup(ms, data, false);
mapptr = gt_fa_mmap_read(filename, &numofbytes, err);
if (mapptr == NULL)
{
had_err = -1;
}
*mapped = mapptr;
if (!had_err)
{
if (assigncorrecttype(ms->mapspectable.spaceGtMapspecification,
mapptr,0,err) != 0)
{
had_err = -1;
}
}
if (!had_err)
{
expectedaccordingtomapspec =
detexpectedaccordingtomapspec(&ms->mapspectable);
if (expectedaccordingtomapspec != (uint64_t) numofbytes)
{
gt_error_set(err, GT_WU " bytes read from %s, but " Formatuint64_t
" expected",
(GtUword) numofbytes,
filename,
PRINTuint64_tcast(expectedaccordingtomapspec));
had_err = -1;
}
}
if (!had_err)
{
mapspecptr = ms->mapspectable.spaceGtMapspecification;
gt_assert(mapspecptr != NULL);
byteoffset = CALLCASTFUNC(uint64_t,unsigned_long,
(uint64_t) (mapspecptr->sizeofunit *
mapspecptr->numofunits));
if (byteoffset % (GtUword) GT_WORDSIZE_INBYTES > 0)
{
size_t padunits
= GT_WORDSIZE_INBYTES - (byteoffset % GT_WORDSIZE_INBYTES);
byteoffset += (GtUword) padunits;
totalpadunits += (GtUword) padunits;
}
for (mapspecptr++;
mapspecptr < ms->mapspectable.spaceGtMapspecification +
ms->mapspectable.nextfreeGtMapspecification; mapspecptr++)
{
if (assigncorrecttype(mapspecptr,mapptr,byteoffset,err) != 0)
{
had_err = -1;
break;
}
byteoffset = CALLCASTFUNC(uint64_t,unsigned_long,
(uint64_t) (byteoffset +
mapspecptr->sizeofunit *
mapspecptr->numofunits));
if (byteoffset % (GtUword) GT_WORDSIZE_INBYTES > 0)
{
size_t padunits
= GT_WORDSIZE_INBYTES - (byteoffset % GT_WORDSIZE_INBYTES);
byteoffset += (GtUword) padunits;
totalpadunits += (GtUword) padunits;
}
}
}
if (!had_err)
{
if (expectedsize + totalpadunits != byteoffset)
{
gt_error_set(err,"mapping: expected file size is "GT_WU" bytes, "
"but file has "GT_WU" bytes",
expectedsize,byteoffset);
had_err = -1;
}
}
GT_FREEARRAY(&ms->mapspectable,GtMapspecification);
gt_free(ms);
return had_err;
}
static int enumeratelcpintervals(const char *inputindex,
Sequentialsuffixarrayreader *ssar,
const char *storeindex,
bool storecounts,
GtUword mersize,
GtUword minocc,
GtUword maxocc,
bool performtest,
GtLogger *logger,
GtError *err)
{
TyrDfsstate *state;
bool haserr = false;
unsigned int alphasize;
gt_error_check(err);
state = gt_malloc(sizeof (*state));
GT_INITARRAY(&state->occdistribution,Countwithpositions);
state->esrspace = gt_encseq_create_reader_with_readmode(
gt_encseqSequentialsuffixarrayreader(ssar),
gt_readmodeSequentialsuffixarrayreader(ssar),
0);
state->mersize = (GtUword) mersize;
state->encseq = gt_encseqSequentialsuffixarrayreader(ssar);
alphasize = gt_alphabet_num_of_chars(gt_encseq_alphabet(state->encseq));
state->readmode = gt_readmodeSequentialsuffixarrayreader(ssar);
state->storecounts = storecounts;
state->minocc = minocc;
state->maxocc = maxocc;
state->totallength = gt_encseq_total_length(state->encseq);
state->performtest = performtest;
state->countoutputmers = 0;
state->merindexfpout = NULL;
state->countsfilefpout = NULL;
GT_INITARRAY(&state->largecounts,Largecount);
if (strlen(storeindex) == 0)
{
state->sizeofbuffer = 0;
state->bytebuffer = NULL;
} else
{
state->sizeofbuffer = MERBYTES(mersize);
state->bytebuffer = gt_malloc(sizeof *state->bytebuffer
* state->sizeofbuffer);
}
if (performtest)
{
state->currentmer = gt_malloc(sizeof *state->currentmer
* state->mersize);
state->suftab = gt_suftabSequentialsuffixarrayreader(ssar);
} else
{
state->currentmer = NULL;
state->suftab = NULL;
}
if (state->mersize > state->totallength)
{
gt_error_set(err,"mersize "GT_WU" > "GT_WU" = totallength not allowed",
state->mersize,
state->totallength);
haserr = true;
} else
{
if (strlen(storeindex) == 0)
{
state->processoccurrencecount = adddistpos2distribution;
} else
{
state->merindexfpout = gt_fa_fopen_with_suffix(storeindex,MERSUFFIX,
"wb",err);
if (state->merindexfpout == NULL)
{
haserr = true;
} else
{
if (state->storecounts)
{
state->countsfilefpout
= gt_fa_fopen_with_suffix(storeindex,COUNTSSUFFIX,"wb",err);
if (state->countsfilefpout == NULL)
{
haserr = true;
}
}
}
state->processoccurrencecount = outputsortedstring2index;
}
if (!haserr)
{
if (gt_depthfirstesa(ssar,
tyr_allocateDfsinfo,
tyr_freeDfsinfo,
tyr_processleafedge,
NULL,
tyr_processcompletenode,
tyr_assignleftmostleaf,
tyr_assignrightmostleaf,
(Dfsstate*) state,
logger,
err) != 0)
{
haserr = true;
}
if (strlen(storeindex) == 0)
{
showfinalstatistics(state,inputindex,logger);
}
}
if (!haserr)
{
if (state->countsfilefpout != NULL)
{
gt_logger_log(logger,"write "GT_WU" mercounts > "GT_WU
" to file \"%s%s\"",
state->largecounts.nextfreeLargecount,
(GtUword) MAXSMALLMERCOUNT,
storeindex,
COUNTSSUFFIX);
gt_xfwrite(state->largecounts.spaceLargecount, sizeof (Largecount),
(size_t) state->largecounts.nextfreeLargecount,
state->countsfilefpout);
}
}
if (!haserr)
{
gt_logger_log(logger,"number of "GT_WU"-mers in index: "GT_WU"",
mersize,
state->countoutputmers);
gt_logger_log(logger,"index size: %.2f megabytes\n",
GT_MEGABYTES(state->countoutputmers * state->sizeofbuffer +
sizeof (GtUword) * EXTRAINTEGERS));
}
}
/* now out EXTRAINTEGERS integer values */
if (!haserr && state->merindexfpout != NULL)
{
outputbytewiseUlongvalue(state->merindexfpout,
(GtUword) state->mersize);
outputbytewiseUlongvalue(state->merindexfpout,(GtUword) alphasize);
}
gt_fa_xfclose(state->merindexfpout);
gt_fa_xfclose(state->countsfilefpout);
GT_FREEARRAY(&state->occdistribution,Countwithpositions);
gt_free(state->currentmer);
gt_free(state->bytebuffer);
GT_FREEARRAY(&state->largecounts,Largecount);
gt_encseq_reader_delete(state->esrspace);
gt_free(state);
return haserr ? -1 : 0;
}
GtBareEncseq *gt_bare_encseq_parse_new(GtUchar *filecontents,size_t numofbytes,
const GtAlphabet *alphabet,
GtError *err)
{
GtUchar *writeptr = filecontents, *readptr = filecontents;
const GtUchar *endptr = filecontents + numofbytes;
bool firstline = true, haserr = false;
GtUword lastspecialrange_length = 0;
GtBareSpecialrange *srptr = NULL;
GtBareEncseq *bare_encseq = gt_malloc(sizeof *bare_encseq);
const GtUchar *smap = gt_alphabet_symbolmap(alphabet);
bare_encseq->specialcharacters = 0;
bare_encseq->numofchars = (GtUword) gt_alphabet_num_of_chars(alphabet);
bare_encseq->charcount = gt_calloc((size_t) bare_encseq->numofchars,
sizeof *bare_encseq->charcount);
GT_INITARRAY(&bare_encseq->specialranges,GtBareSpecialrange);
readptr = filecontents;
while (!haserr && readptr < endptr)
{
if (*readptr == '>')
{
if (!firstline)
{
if (lastspecialrange_length == 0)
{
GT_GETNEXTFREEINARRAY(srptr,&bare_encseq->specialranges,
GtBareSpecialrange,128UL);
srptr->start = (GtUword) (writeptr - filecontents);
}
lastspecialrange_length++;
*writeptr++ = SEPARATOR;
bare_encseq->specialcharacters++;
} else
{
firstline = false;
}
while (readptr < endptr && *readptr != '\n')
{
readptr++;
}
readptr++;
} else
{
while (readptr < endptr && *readptr != '\n')
{
if (!isspace(*readptr))
{
GtUchar cc = smap[*readptr];
if (cc == UNDEFCHAR)
{
gt_error_set(err,"illegal input characters %c\n",*readptr);
haserr = true;
break;
}
if (ISSPECIAL(cc))
{
if (lastspecialrange_length == 0)
{
GT_GETNEXTFREEINARRAY(srptr,&bare_encseq->specialranges,
GtBareSpecialrange,128UL);
srptr->start = (GtUword) (writeptr - filecontents);
}
lastspecialrange_length++;
bare_encseq->specialcharacters++;
} else
{
gt_assert((GtUword) cc < bare_encseq->numofchars);
bare_encseq->charcount[(int) cc]++;
if (lastspecialrange_length > 0)
{
gt_assert(srptr != NULL);
srptr->length = lastspecialrange_length;
}
lastspecialrange_length = 0;
}
*writeptr++ = cc;
}
readptr++;
}
readptr++;
}
}
if (lastspecialrange_length > 0)
{
gt_assert(srptr != NULL);
srptr->length = lastspecialrange_length;
}
bare_encseq->sequence = filecontents;
bare_encseq->totallength = (GtUword) (writeptr - filecontents);
if (haserr)
{
gt_bare_encseq_delete(bare_encseq);
return NULL;
}
return bare_encseq;
}