void print_maf_match
(FILE* f,
seq* seq1,
unspos pos1,
seq* seq2,
unspos pos2,
unspos length,
score s,
int withComments)
{
seqpartition* sp1 = &seq1->partition;
seqpartition* sp2 = &seq2->partition;
partition* part;
u8* s1 = seq1->v + pos1;
u8* s2 = seq2->v + pos2;
char* name1, *name2, *pref2, *suff1, *suff2;
unspos offset1, offset2, start1, start2;
unspos startLoc1, startLoc2;
unspos seq1Len, seq2Len, seq1True, seq2True;
char strand1, strand2;
int len1, len2, nameW, startW, lenW;
unspos ix;
segment seg;
unspos numer, denom;
if (seq1->revCompFlags != rcf_forward)
suicide ("attempt to print - strand or complement for sequence 1 in print_maf_match");
#ifdef debugSeq1Beg
if ((pos1 < debugSeq1Beg) || (pos1+length > debugSeq1End)) return;
#endif // debugSeq1Beg
// report diagonal
if (maf_dbgReportDiag)
fprintf (f, "# diagonal=" sgnposFmt "\n", diagNumber(pos1,pos2));
if (withComments)
{
// report identity
segment_identity (seq1, pos1, seq2, pos2, length, &numer, &denom);
fprintf (f, "# identity=" unsposSlashFmt, numer, denom);
if (denom != 0) fprintf (f, " (%.1f%%)", (100.0*numer) / denom);
fprintf (f, "\n");
// report coverage
seg.pos1 = pos1;
seg.pos2 = pos2;
seg.length = length;
segment_coverage (seq1, seq2, &seg, &numer, &denom);
fprintf (f, "# coverage=" unsposSlashFmt, numer, denom);
if (denom != 0) fprintf (f, " (%.1f%%)", (100.0*numer) / denom);
fprintf (f, "\n");
// report alignment path
fprintf (f, "# cigar=" unsposFmt "m\n", length);
}
// figure out position offsets and names
if (sp1->p == NULL) // sequence 1 is not partitioned
{
name1 = (seq1->useFullNames)? seq1->header : seq1->shortHeader;
if ((name1 == NULL) || (name1[0] == 0)) name1 = "seq1";
offset1 = 0;
startLoc1 = seq1->startLoc;
seq1Len = seq1->len;
seq1True = seq1->trueLen;
}
else // sequence 1 is partitioned
{
part = lookup_partition (seq1, pos1);
name1 = &sp1->pool[part->header];
offset1 = part->sepBefore + 1;
startLoc1 = part->startLoc;
seq1Len = part->sepAfter - offset1;
seq1True = part->trueLen;
}
if (sp2->p == NULL) // sequence 2 is not partitioned
{
name2 = (seq2->useFullNames)? seq2->header : seq2->shortHeader;
if ((name2 == NULL) || (name2[0] == 0)) name2 = "seq2";
offset2 = 0;
startLoc2 = seq2->startLoc;
seq2Len = seq2->len;
seq2True = seq2->trueLen;
}
else // sequence 2 is partitioned
{
part = lookup_partition (seq2, pos2);
name2 = &sp2->pool[part->header];
offset2 = part->sepBefore + 1;
startLoc2 = part->startLoc;
seq2Len = part->sepAfter - offset2;
seq2True = part->trueLen;
}
// print summary line
fprintf (f, "a score=" scoreFmt "\n", s);
// figure out fields and widths
pref2 = ((maf_distinguishNames) && (strcmp (name1, name2) == 0))? "~" : "";
suff1 = rcfSuffix[seq1->revCompFlags];
suff2 = rcfSuffix[seq2->revCompFlags];
if ((seq1->revCompFlags & rcf_rev) == 0)
{
start1 = pos1 - offset1 + startLoc1;
strand1 = '+';
}
else
{
start1 = pos1 - offset1 + seq1True+2 - (startLoc1 + seq1Len);
strand1 = '-';
}
if ((seq2->revCompFlags & rcf_rev) == 0)
{
start2 = pos2 - offset2 + startLoc2;
strand2 = '+';
}
else
{
start2 = pos2 - offset2 + seq2True+2 - (startLoc2 + seq2Len);
strand2 = '-';
}
len1 = strlen (name1) + strlen (suff1);
len2 = strlen (pref2) + strlen (name2) + strlen (suff2);
nameW = (len1 >= len2)? len1 : len2;
startW = max_digits (start1, start2);
lenW = max_digits (seq1True, seq2True);
// print aligning segment of sequence 1 (non-printables are printed as '*'
// but such should never be seen unless there is a problem elsewhere)
fprintf (f, "s %s%s%*s" unsposStarFmt " " unsposFmt " %c " unsposStarFmt " ",
name1, suff1, nameW+1-len1, " ",
startW, start1-1, length, strand1, lenW, seq1True);
for (ix=0 ; ix<length ; ix++)
fprintf (f, "%c", dna_toprint(s1[ix]));
fprintf (f, "\n");
// print aligning segment of sequence 2
fprintf (f, "s %s%s%s%*s" unsposStarFmt " " unsposFmt " %c " unsposStarFmt " ",
pref2, name2, suff2, nameW+1-len2, " ",
startW, start2-1, length, strand2, lenW, seq2True);
for (ix=0 ; ix<length ; ix++)
fprintf (f, "%c", dna_toprint(s2[ix]));
fprintf (f, "\n\n");
}
void print_match (unspos pos1, unspos pos2, unspos length, score s)
// pos1 and pos2 are the positions of first character in the match,
// .. (origin-0).
{
static u32 printsUntilFlush = matchFlushFrequency;
int outputFormat = currParams->outputFormat;
if ((currParams->searchLimit > 0)
&& (printedForQuery >= currParams->searchLimit))
return;
printedForQuery++;
if (!strandHeaderPrinted)
{ print_header (); strandHeaderPrinted = true; }
if (infer_scores_dbgShowIdentity)
{
unspos numer, denom;
u32 bin;
segment_identity (currParams->seq1, pos1, currParams->seq2, pos2, length,
&numer, &denom);
bin = identity_bin (numer, denom);
// nota bene: positions written as 1-based
print_generic (currParams->outputFile,
unsposSlashFmt
" pct_identity=" unsposSlashFmt
" (bin as " identityBinFormat ")",
pos1+1, pos2+1,
numer, denom,
bin_to_identity (bin));
}
switch (outputFormat)
{
case fmtGfa:
case fmtGfaNoScore:
print_gfa_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
(outputFormat == fmtGfa)? s : 0);
break;
case fmtLav:
case fmtLavComment:
case fmtLavText:
case fmtLavInfScores:
print_lav_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s);
if (outputFormat == fmtLavText)
goto text_format;
if (outputFormat == fmtLavInfScores)
goto inf_scores_format;
break;
case fmtLavScore:
print_lavscore_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s);
break;
case fmtAxt:
case fmtAxtComment:
print_axt_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s,
/* comments */ outputFormat==fmtAxtComment,
/* extras */ NULL);
break;
case fmtAxtGeneral:
print_axt_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s,
/* comments */ false,
/* extras */ currParams->outputInfo);
break;
case fmtMaf:
case fmtMafNoComment:
print_maf_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s, /* comments */ false);
break;
case fmtMafComment:
print_maf_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s, /* comments */ true);
break;
case fmtSoftSam:
case fmtSoftSamNoHeader:
print_sam_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s,
/* softMasking */ true,
currParams->samRGTags);
break;
case fmtHardSam:
case fmtHardSamNoHeader:
print_sam_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s,
/* softMasking */ false,
currParams->samRGTags);
break;
case fmtCigar:
print_cigar_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s,
/* withInfo */ true,
/* markMismatches */ false,
/* letterAfter */ false,
/* hideSingles */ false,
/* lowerCase */ false,
/* withNewLine */ true);
break;
case fmtGenpaf:
case fmtGenpafNoHeader:
case fmtGenpafNameHeader:
case fmtGenpafBlast:
case fmtGenpafBlastNoHeader:
print_genpaf_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s, currParams->outputInfo);
break;
case fmtText:
case fmtZeroText:
text_format:
print_text_align_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s,
(outputFormat!=fmtZeroText),
currParams->textContext);
break;
case fmtDiffs:
case fmtDiffsNoBlocks:
print_align_diffs_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
(outputFormat == fmtDiffs),
currParams->nIsAmbiguous);
break;
case fmtHspComp:
print_match_composition (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s, currParams->hitSeed, currParams->step);
break;
case fmtInfStats:
infer_stats_from_match (currParams->seq1, pos1,
currParams->seq2, pos2, length);
break;
case fmtInfScores:
inf_scores_format:
gather_stats_from_match (currParams->seq1, pos1,
currParams->seq2, pos2, length);
break;
case fmtIdDist:
identity_dist_from_match (currParams->seq1, pos1,
currParams->seq2, pos2, length);
break;
case fmtDeseed:
dump_match (currParams->outputFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length);
printf ("\n");
break;
case fmtNone:
; // (do nothing)
break;
default:
suicidef ("internal error, in print_match, outputFormat=%d", outputFormat);
}
if (currParams->dotplotFile != NULL)
print_genpaf_match (currParams->dotplotFile,
currParams->seq1, pos1,
currParams->seq2, pos2, length,
s, currParams->dotplotKeys);
if (--printsUntilFlush == 0)
{
fflush (currParams->outputFile);
printsUntilFlush = matchFlushFrequency;
}
}