void gt_alignment_show_generic(GtUchar *buffer,
bool downcase,
const GtAlignment *alignment,
FILE *fp,
unsigned int width,
const GtUchar *characters,
GtUchar wildcardshow)
{
GtMultieop meop;
GtUword idx_eop, idx_u = 0, idx_v = 0, meoplen, alignmentlength = 0,
suffix_bits_used = 0, prefix_positive = 0, pol_size = 0,
firstseedcolumn = GT_UWORD_MAX,
lastseedcolumn = GT_UWORD_MAX;
const GtUword max_history = 64;
unsigned int pos = 0;
GtUchar *topbuf = buffer, *midbuf = NULL, *lowbuf = NULL;
GtWord prefix_positive_sum = 0;
uint64_t suffix_bits = 0, set_mask = 0;
if (alignment->pol_info != NULL)
{
pol_size = GT_MULT2(alignment->pol_info->cut_depth);
set_mask = ((uint64_t) 1) << (max_history - 1);
}
gt_assert(alignment != NULL && (characters == NULL || !downcase));
topbuf[width] = '\n';
midbuf = topbuf + width + 1;
midbuf[width] = '\n';
lowbuf = midbuf + width + 1;
lowbuf[width] = '\n';
meoplen = gt_multieoplist_get_num_entries(alignment->eops);
gt_assert(meoplen > 0);
idx_eop = meoplen - 1;
while (true)
{
meop = gt_multieoplist_get_entry(alignment->eops, idx_eop);
switch (meop.type)
{
GtUword j;
case Mismatch:
case Match:
case Replacement:
for (j = 0; j < meop.steps && idx_u < alignment->ulen &&
idx_v < alignment->vlen; j++)
{
GtUchar a = alignment->u[idx_u];
GtUchar b = alignment->v[idx_v];
bool is_match;
if (characters != NULL)
{
topbuf[pos] = ISSPECIAL(a) ? wildcardshow : characters[a];
is_match = (a == b && !ISSPECIAL(a)) ? true : false;
lowbuf[pos] = ISSPECIAL(b) ? wildcardshow : characters[b];
} else
{
topbuf[pos] = a;
is_match = ((downcase && tolower((int) a) == tolower((int) b)) ||
(!downcase && a == b)) ? true : false;
lowbuf[pos] = b;
}
if (is_match)
{
if (alignment->useedoffset <= idx_u &&
idx_u < alignment->useedoffset + alignment->seedlen)
{
if (alignment->seed_display)
{
midbuf[pos] = (GtUchar) '+';
} else
{
midbuf[pos] = (GtUchar) MATCHSYMBOL;
}
if (firstseedcolumn == GT_UWORD_MAX)
{
firstseedcolumn = alignmentlength;
}
lastseedcolumn = alignmentlength;
} else
{
midbuf[pos] = (GtUchar) MATCHSYMBOL;
}
} else
{
midbuf[pos] = (GtUchar) MISMATCHSYMBOL;
}
pos = gt_alignment_show_advance(pos,width,topbuf,fp);
GT_UPDATE_POSITIVE_INFO(is_match);
alignmentlength++;
idx_u++;
idx_v++;
}
break;
case Deletion:
for (j = 0; j < meop.steps && idx_u < alignment->ulen; j++)
{
GtUchar a = alignment->u[idx_u++];
if (characters != NULL)
{
topbuf[pos] = ISSPECIAL(a) ? wildcardshow : characters[a];
} else
{
topbuf[pos] = a;
}
midbuf[pos] = (GtUchar) MISMATCHSYMBOL;
lowbuf[pos] = (GtUchar) GAPSYMBOL;
pos = gt_alignment_show_advance(pos,width,topbuf,fp);
GT_UPDATE_POSITIVE_INFO(false);
alignmentlength++;
}
break;
case Insertion:
for (j = 0; j < meop.steps && idx_v < alignment->vlen; j++)
{
GtUchar b = alignment->v[idx_v++];
topbuf[pos] = (GtUchar) GAPSYMBOL;
midbuf[pos] = (GtUchar) MISMATCHSYMBOL;
if (characters != NULL)
{
lowbuf[pos] = ISSPECIAL(b) ? wildcardshow : characters[b];
} else
{
lowbuf[pos] = b;
}
pos = gt_alignment_show_advance(pos,width,topbuf,fp);
GT_UPDATE_POSITIVE_INFO(false);
alignmentlength++;
}
break;
}
if (idx_eop > 0 && (idx_u < alignment->ulen || idx_v < alignment->vlen))
{
idx_eop--;
} else
{
break;
}
}
if (pos > 0)
{
topbuf[pos] = '\n';
fwrite(topbuf,sizeof *topbuf,pos+1,fp);
midbuf[pos] = '\n';
fwrite(midbuf,sizeof *midbuf,pos+1,fp);
lowbuf[pos] = '\n';
fwrite(lowbuf,sizeof *lowbuf,pos+1,fp);
}
if (alignment->pol_info != NULL)
{
GtUword suffix_positive;
GtWord suffix_positive_sum = 0;
bool startpolished = false, endpolished = false;
for (suffix_positive = 0; suffix_positive < suffix_bits_used;
suffix_positive++)
{
suffix_positive_sum += ((suffix_bits & set_mask)
? alignment->pol_info->match_score
: -alignment->pol_info->difference_score);
if (suffix_positive_sum < 0)
{
break;
}
set_mask >>= 1;
}
gt_assert(prefix_positive <= alignmentlength &&
prefix_positive <= alignmentlength);
if (prefix_positive >= pol_size || prefix_positive == alignmentlength ||
firstseedcolumn < pol_size)
{
startpolished = true;
}
if (suffix_positive >= pol_size || suffix_positive == alignmentlength ||
(lastseedcolumn != GT_UWORD_MAX &&
lastseedcolumn + pol_size > alignmentlength))
{
endpolished = true;
}
printf("# polishing(m=" GT_WD ",d=" GT_WD ",p=" GT_WU
"): " GT_WU "/" GT_WU,
alignment->pol_info->match_score,
-alignment->pol_info->difference_score,
pol_size,
prefix_positive,
suffix_positive);
if (firstseedcolumn < pol_size)
{
printf(", seed_on_start");
}
if (lastseedcolumn + pol_size > alignmentlength)
{
printf(", seed_on_end");
}
if (alignment->withpolcheck)
{
printf("\n");
gt_assert(startpolished && endpolished);
} else
{
if (!startpolished)
{
printf(", start not polished");
}
if (!endpolished)
{
printf(", end not polished");
}
printf("\n");
}
}
void gt_eoplist_format_generic(FILE *fp,
const GtEoplist *eoplist,
GtEoplistReader *eoplist_reader,
bool distinguish_mismatch_match,
const GtUchar *characters,
GtUchar wildcardshow)
{
GtCigarOp co;
unsigned int pos = 0;
GtUword idx_u = 0, idx_v = 0, alignmentlength = 0,
firstseedcolumn = GT_UWORD_MAX;
GtUchar *topbuf = eoplist_reader->outbuffer, *midbuf = NULL, *lowbuf = NULL;
#ifndef OUTSIDE_OF_GT
uint64_t suffix_bits = 0, set_mask = 0;
GtUword suffix_bits_used = 0, prefix_positive = 0, pol_size = 0,
lastseedcolumn = GT_UWORD_MAX;
const GtUword max_history = 64;
GtWord prefix_positive_sum = 0;
if (eoplist->pol_info != NULL)
{
pol_size = GT_MULT2(eoplist->pol_info->cut_depth);
set_mask = ((uint64_t) 1) << (max_history - 1);
}
#endif
gt_assert(eoplist_reader != NULL);
topbuf[eoplist_reader->width] = '\n';
midbuf = topbuf + eoplist_reader->width + 1;
midbuf[eoplist_reader->width] = '\n';
lowbuf = midbuf + eoplist_reader->width + 1;
lowbuf[eoplist_reader->width] = '\n';
gt_eoplist_reader_reset(eoplist_reader,eoplist);
if (distinguish_mismatch_match)
{
gt_eoplist_reader_distinguish_mismatch_match(eoplist_reader);
}
while (gt_eoplist_reader_next_cigar(&co,eoplist_reader))
{
switch (co.eoptype)
{
GtUword j;
GtUchar cc_a, cc_b;
case GtMatchOp:
case GtMismatchOp:
for (j = 0; j < co.iteration && idx_u < eoplist->ulen &&
idx_v < eoplist->vlen; j++)
{
cc_a = eoplist->useq[idx_u];
cc_b = eoplist->vseq[idx_v];
bool is_match;
if (characters != NULL)
{
topbuf[pos] = ISSPECIAL(cc_a) ? wildcardshow : characters[cc_a];
lowbuf[pos] = ISSPECIAL(cc_b) ? wildcardshow : characters[cc_b];
is_match = (cc_a == cc_b && !ISSPECIAL(cc_a)) ? true : false;
} else
{
topbuf[pos] = cc_a;
is_match = (cc_a == cc_b) ? true : false;
lowbuf[pos] = cc_b;
}
if (is_match)
{
if (eoplist->useedoffset <= idx_u &&
idx_u < eoplist->useedoffset + eoplist->seedlen)
{
if (eoplist->seed_display)
{
midbuf[pos] = (GtUchar) '+';
} else
{
midbuf[pos] = (GtUchar) EOPLIST_MATCHSYMBOL;
}
if (firstseedcolumn == GT_UWORD_MAX)
{
firstseedcolumn = alignmentlength;
}
#ifndef OUTSIDE_OF_GT
lastseedcolumn = alignmentlength;
#endif
} else
{
midbuf[pos] = (GtUchar) EOPLIST_MATCHSYMBOL;
}
} else
{
midbuf[pos] = (GtUchar) EOPLIST_MISMATCHSYMBOL;
}
pos = gt_eoplist_show_advance(pos,eoplist_reader->width,topbuf,fp);
GT_UPDATE_POSITIVE_INFO(is_match);
alignmentlength++;
idx_u++;
idx_v++;
}
break;
case GtDeletionOp:
for (j = 0; j < co.iteration && idx_u < eoplist->ulen; j++)
{
cc_a = eoplist->useq[idx_u++];
if (characters != NULL)
{
topbuf[pos] = ISSPECIAL(cc_a) ? wildcardshow : characters[cc_a];
} else
{
topbuf[pos] = cc_a;
}
midbuf[pos] = EOPLIST_MISMATCHSYMBOL;
lowbuf[pos] = EOPLIST_GAPSYMBOL;
pos = gt_eoplist_show_advance(pos,eoplist_reader->width,topbuf,fp);
GT_UPDATE_POSITIVE_INFO(false);
alignmentlength++;
}
break;
case GtInsertionOp:
for (j = 0; j < co.iteration && idx_v < eoplist->vlen; j++)
{
cc_b = eoplist->vseq[idx_v++];
topbuf[pos] = EOPLIST_GAPSYMBOL;
midbuf[pos] = EOPLIST_MISMATCHSYMBOL;
if (characters != NULL)
{
lowbuf[pos] = ISSPECIAL(cc_b) ? wildcardshow : characters[cc_b];
} else
{
lowbuf[pos] = cc_b;
}
pos = gt_eoplist_show_advance(pos,eoplist_reader->width,topbuf,fp);
GT_UPDATE_POSITIVE_INFO(false);
alignmentlength++;
}
break;
default:
fprintf(stderr,"file %s, line %d: illegal eoptype %d\n",
__FILE__,__LINE__,co.eoptype);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
}
if (pos > 0)
{
topbuf[pos] = '\n';
fwrite(topbuf,sizeof *topbuf,pos+1,fp);
midbuf[pos] = '\n';
fwrite(midbuf,sizeof *midbuf,pos+1,fp);
lowbuf[pos] = '\n';
fwrite(lowbuf,sizeof *lowbuf,pos+1,fp);
}
#ifndef OUTSIDE_OF_GT
if (eoplist->pol_info != NULL)
{
GtUword suffix_positive;
GtWord suffix_positive_sum = 0;
bool startpolished = false, endpolished = false;
for (suffix_positive = 0; suffix_positive < suffix_bits_used;
suffix_positive++)
{
suffix_positive_sum += ((suffix_bits & set_mask)
? eoplist->pol_info->match_score
: -eoplist->pol_info->difference_score);
if (suffix_positive_sum < 0)
{
break;
}
set_mask >>= 1;
}
gt_assert(prefix_positive <= alignmentlength);
if (prefix_positive >= pol_size || prefix_positive == alignmentlength ||
firstseedcolumn < pol_size)
{
startpolished = true;
}
if (suffix_positive >= pol_size || suffix_positive == alignmentlength ||
(lastseedcolumn != GT_UWORD_MAX &&
lastseedcolumn + pol_size > alignmentlength))
{
endpolished = true;
}
fprintf(fp, "# polishing(m=" GT_WD ",d=" GT_WD ",p=" GT_WU
"): " GT_WU "/" GT_WU,
eoplist->pol_info->match_score,
-eoplist->pol_info->difference_score,
pol_size,
prefix_positive,
suffix_positive);
if (firstseedcolumn < pol_size)
{
fprintf(fp, ", seed_on_start");
}
if (lastseedcolumn + pol_size > alignmentlength)
{
fprintf(fp, ", seed_on_end");
}
if (eoplist->withpolcheck)
{
fprintf(fp, "\n");
gt_assert(startpolished);
gt_assert(endpolished);
} else
{
if (!startpolished)
{
fprintf(fp, ", start not polished");
}
if (!endpolished)
{
fprintf(fp, ", end not polished");
}
fprintf(fp, "\n");
}
}
