Commit 7de1d067 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

core/{segment,windowExtractor}.cpp: display .affect on several lines, one...

core/{segment,windowExtractor}.cpp: display .affect on several lines, one character by affect, and bikeshedding

closes #4727
parent ea24ae0a
......@@ -431,13 +431,20 @@ string KmerSegmenter::getInfoLineWithAffects() const
{
stringstream ss;
ss << "# "
ss << "= " << right << setw(10) << segmented_germline->code << " "
<< right << setw(3) << score << " "
<< left << setw(30)
<< getInfoLine() ;
<< getInfoLine();
if (getSegmentationStatus() != UNSEG_TOO_SHORT)
ss << getKmerAffectAnalyser()->toString();
{
ss << endl;
ss << "# " << right << setw(10) << segmented_germline->code << " "
<< getKmerAffectAnalyser()->toStringValues();
ss << endl;
ss << "$ " << right << setw(10) << segmented_germline->code << " "
<< getKmerAffectAnalyser()->toStringSigns();
}
return ss.str();
}
......
......@@ -53,7 +53,8 @@ WindowsStorage *WindowExtractor::extract(OnlineBioReader *reads,
nb_reads++;
if (out_affects) {
*out_affects << reads->getSequence();
Sequence seq = reads->getSequence();
*out_affects << ">" << setw(11) << left << seq.label << " " << seq.sequence << endl;
}
KmerMultiSegmenter kmseg(reads->getSequence(), multigermline, out_affects, nb_expected, nb_reads_for_evalue);
......@@ -114,7 +115,7 @@ WindowsStorage *WindowExtractor::extract(OnlineBioReader *reads,
// Last line of detailed affects output
if (out_affects) {
*out_affects << "#>" << seg->label << " " << seg->getInfoLine() << endl << endl;
*out_affects << "==> " << seg->label << " " << seg->getInfoLine() << endl << endl;
}
// Progress bar
......
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