static int outputsortedstring2indexviafileptr(const GtEncseq *encseq,
GtUword mersize,
GtUchar *bytebuffer,
GtUword sizeofbuffer,
FILE *merindexfpout,
FILE *countsfilefpout,
GtUword position,
GtUword countocc,
GtArrayLargecount *largecounts,
GtUword countoutputmers,
GT_UNUSED GtError *err)
{
gt_encseq_sequence2bytecode(bytebuffer,encseq,position,mersize);
gt_xfwrite(bytebuffer, sizeof (*bytebuffer), (size_t) sizeofbuffer,
merindexfpout);
if (countsfilefpout != NULL)
{
GtUchar smallcount;
if (countocc <= MAXSMALLMERCOUNT)
{
smallcount = (GtUchar) countocc;
} else
{
Largecount *lc;
GT_GETNEXTFREEINARRAY(lc,largecounts,Largecount,32);
lc->idx = countoutputmers;
lc->value = countocc;
smallcount = 0;
}
gt_xfwrite(&smallcount, sizeof (smallcount),(size_t) 1,countsfilefpout);
}
return 0;
}
void gt_wlis_filter_matches_add(GtWLisFilterMatches *wlismatches,
GtUword s_start, GtUword s_end,
GtUword q_start, GtUword q_end,
GtUword distance,
bool store_querymatch)
{
GtUword aligned_len;
float prob_id;
GtWlisItem *current_match;
gt_assert(wlismatches != NULL);
GT_GETNEXTFREEINARRAY(current_match,&wlismatches->items,GtWlisItem,
wlismatches->items.
allocatedGtWlisItem * 0.2 + 256);
current_match->startpos[0] = s_start;
current_match->startpos[1] = q_start;
current_match->endpos[0] = s_end;
current_match->endpos[1] = q_end;
if (store_querymatch)
{
gt_assert(wlismatches->items.nextfreeGtWlisItem > 0);
current_match->oi_di.original_index
= wlismatches->items.nextfreeGtWlisItem - 1;
} else
{
current_match->oi_di.distance = distance;
}
aligned_len = gt_wlis_filter_aligned_len(current_match);
prob_id = (float) (aligned_len - 2 * distance)/aligned_len;
current_match->weight = prob_id * prob_id;
}
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;
}
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;
}
