void print_maf_align_list
(FILE* f,
alignel* alignList,
seq* seq1,
seq* seq2,
int withComments)
{
alignel* a;
unspos numer, denom;
for (a=alignList ; a!=NULL ; a=a->next)
{
if (withComments)
{
unspos height, width, i, j, prevI, prevJ, run;
u32 opIx;
// report identity
alignment_identity (seq1, seq2, a, &numer, &denom);
fprintf (f, "# identity=" unsposSlashFmt, numer, denom);
if (denom != 0) fprintf (f, " (%.1f%%)", (100.0*numer) / denom);
fprintf (f, "\n");
// report coverage
alignment_coverage (seq1, seq2, a, &numer, &denom);
fprintf (f, "# coverage=" unsposSlashFmt, numer, denom);
if (denom != 0) fprintf (f, " (%.1f%%)", (100.0*numer) / denom);
fprintf (f, "\n");
// report continuity
alignment_continuity (a, &numer, &denom);
fprintf (f, "# continuity=" unsposSlashFmt, numer, denom);
if (denom != 0) fprintf (f, " (%.1f%%)", (100.0*numer) / denom);
fprintf (f, "\n");
// report alignment path
fprintf (f, "# cigar=");
height = a->end1 - a->beg1 + 1;
width = a->end2 - a->beg2 + 1;
opIx = 0;
for (i=j=0 ; (i< height)||(j<width) ; )
{
run = edit_script_run_of_subs (a->script, &opIx);
fprintf (f, unsposFmt "m", run);
i += run; j += run;
if ((i < height) || (j < width))
{
prevI = i; prevJ = j;
edit_script_indel_len (a->script, &opIx, &i, &j);
if (i > prevI)
fprintf (f, unsposFmt "d", i - prevI);
if (j > prevJ)
fprintf (f, unsposFmt "i", j - prevJ);
}
}
fprintf (f, "\n");
}
print_maf_align (f,
seq1, a->beg1-1, a->end1,
seq2, a->beg2-1, a->end2,
a->script, a->s);
}
}
void print_align_list (alignel* alignList)
{
int outputFormat = currParams->outputFormat;
alignel* a;
if ((currParams->searchLimit > 0)
&& (printedForQuery >= currParams->searchLimit))
return;
printedForQuery++;
if (!strandHeaderPrinted)
{ print_header (); strandHeaderPrinted = true; }
if (infer_scores_dbgShowIdentity)
{
unspos numer, denom;
u32 bin;
for (a=alignList ; a!=NULL ; a=a->next)
{
alignment_identity (currParams->seq1, currParams->seq2, a,
&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 ")",
a->beg1, a->beg2,
numer, denom,
bin_to_identity (bin));
}
}
switch (outputFormat)
{
case fmtGfa:
case fmtGfaNoScore:
print_gfa_align_list (currParams->outputFile,
(outputFormat == fmtGfa)? currParams->scoring
: NULL,
alignList,
currParams->seq1, currParams->seq2);
break;
case fmtLav:
case fmtLavComment:
case fmtLavScore:
case fmtLavInfScores:
print_lav_align_list (currParams->outputFile,
alignList,
currParams->seq1, currParams->seq2);
if (outputFormat == fmtLavInfScores)
goto inf_scores_format;
break;
case fmtLavText:
for (a=alignList ; a!=NULL ; a=a->next)
{
print_lav_align (currParams->outputFile,
a->seq1, a->beg1-1, a->end1,
a->seq2, a->beg2-1, a->end2,
a->script, a->s);
print_text_align_align (currParams->outputFile,
currParams->seq1, a->beg1-1, a->end1,
currParams->seq2, a->beg2-1, a->end2,
a->script, a->s,
false, currParams->textContext);
}
break;
case fmtAxt:
case fmtAxtComment:
print_axt_align_list (currParams->outputFile, alignList,
currParams->seq1, currParams->seq2,
/* comments */ outputFormat==fmtAxtComment,
/* extras */ NULL);
break;
case fmtAxtGeneral:
print_axt_align_list (currParams->outputFile, alignList,
currParams->seq1, currParams->seq2,
/* comments */ false,
/* extras */ currParams->outputInfo);
break;
case fmtMaf:
case fmtMafNoComment:
print_maf_align_list (currParams->outputFile,
alignList, currParams->seq1, currParams->seq2,
/* comments */ false);
break;
case fmtMafComment:
print_maf_align_list (currParams->outputFile,
alignList, currParams->seq1, currParams->seq2,
/* comments */ true);
break;
case fmtSoftSam:
case fmtSoftSamNoHeader:
print_sam_align_list (currParams->outputFile,
alignList, currParams->seq1, currParams->seq2,
/* softMasking */ true,
currParams->samRGTags);
break;
case fmtHardSam:
case fmtHardSamNoHeader:
print_sam_align_list (currParams->outputFile,
alignList, currParams->seq1, currParams->seq2,
/* softMasking */ false,
currParams->samRGTags);
break;
case fmtCigar:
print_cigar_align_list (currParams->outputFile,
alignList, currParams->seq1, currParams->seq2,
/* 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_align_list (currParams->outputFile,
alignList, currParams->seq1, currParams->seq2,
currParams->outputInfo);
break;
case fmtText:
case fmtZeroText:
print_text_align_align_list (currParams->outputFile,
alignList, currParams->seq1, currParams->seq2,
(outputFormat!=fmtZeroText),
currParams->textContext);
break;
case fmtDiffs:
case fmtDiffsNoBlocks:
print_align_diffs_align_list (currParams->outputFile,
alignList, currParams->seq1, currParams->seq2,
(outputFormat == fmtDiffs),
currParams->nIsAmbiguous);
break;
case fmtInfStats:
infer_stats_from_align_list (alignList, currParams->seq1, currParams->seq2);
break;
case fmtInfScores:
inf_scores_format:
gather_stats_from_align_list (alignList, currParams->seq1, currParams->seq2);
break;
case fmtIdDist:
identity_dist_from_align_list (alignList, currParams->seq1, currParams->seq2);
break;
case fmtHspComp:
case fmtDeseed:
case fmtNone:
; // (do nothing)
break;
default:
suicidef ("internal error, in print_align_list, outputFormat=%d", outputFormat);
}
if (currParams->dotplotFile != NULL)
print_genpaf_align_list_segments (currParams->dotplotFile,
alignList, currParams->seq1, currParams->seq2,
currParams->dotplotKeys,
currParams->scoring);
}
