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

algo/core/segment.cpp

@@ -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();
 }

algo/core/windowExtractor.cpp

@@ -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