core/windowExtractor.cpp, core/segment.cpp: better '-u' debug

Now 'out_unsegmented' causes are output in segment.cpp, displaying affectation for each germline

algo/core/segment.cpp

@@ -246,7 +246,7 @@ KmerSegmenter::~KmerSegmenter() {
   //   delete kaa;
 }
 
-KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermline)
+KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermline, ostream *out_unsegmented)
 {
   int best_score = 0 ;
   
@@ -257,6 +257,18 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
 
       KmerSegmenter kseg(seq, germline);
 
+      if (out_unsegmented)
+        {
+          // Debug, display k-mer affectation and segmentation result for this germline
+          *out_unsegmented << "#"
+                           << left << setw(4) << kseg.segmented_germline->code << " "
+                           << left << setw(20) << segmented_mesg[kseg.getSegmentationStatus()] << " ";
+          if (kseg.getSegmentationStatus() != UNSEG_TOO_SHORT) 
+            *out_unsegmented << kseg.getKmerAffectAnalyser()->toString();
+
+          *out_unsegmented << endl ;
+        }
+
       if (!best_score)
         the_kseg = kseg;
       

algo/core/segment.h

@@ -179,7 +179,7 @@ class KmerMultiSegmenter
    * @param seq: An object read from a FASTA/FASTQ file
    * @param multigermline: the multigermline
    */
-  KmerMultiSegmenter(Sequence seq, MultiGermline *multigermline);
+  KmerMultiSegmenter(Sequence seq, MultiGermline *multigermline, ostream *out_unsegmented);
   ~KmerMultiSegmenter();
 
   KmerSegmenter the_kseg;

algo/core/windowExtractor.cpp

@@ -20,8 +20,12 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
   while (reads->hasNext()) {
     reads->next();
     nb_reads++;
+
+    if (out_unsegmented) {      
+      *out_unsegmented << reads->getSequence();
+    }
     
-    KmerMultiSegmenter kmseg(reads->getSequence(), multigermline);
+    KmerMultiSegmenter kmseg(reads->getSequence(), multigermline, out_unsegmented);
     
     KmerSegmenter seg = kmseg.the_kseg ;
     int read_length = seg.getSequence().sequence.length();
@@ -43,18 +47,16 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
       if (out_segmented) {
         *out_segmented << seg ; // KmerSegmenter output (V/N/J)
 
-        if (out_unsegmented)
+        if (out_unsegmented) {
 	  *out_segmented << seg.getKmerAffectAnalyser()->toString() << endl;
+          *out_unsegmented << "#>" << reads->getSequence().label << " segmented on " << seg.segmented_germline->code << endl << endl;
+        }
       }
       
       nb_reads_germline[seg.system]++;
       
     } else if (out_unsegmented) {
-      *out_unsegmented << reads->getSequence();
-      *out_unsegmented << "#" << segmented_mesg[seg.getSegmentationStatus()] << " " << seg.segmented_germline->code << endl;
-      if (seg.getSegmentationStatus() != UNSEG_TOO_SHORT) {
-        *out_unsegmented << seg.getKmerAffectAnalyser()->toString() << endl;
-      }
+      *out_unsegmented << "#>" << reads->getSequence().label << " not segmented" << endl << endl;
     }
   }
   return windowsStorage;