core/segment.h: macro rename, UNSEG_TOO_SHORT_FOR_WINDOWS

To be too short for the window is just a non-segmentation/non-analysis cause.

algo/core/segment.h

@@ -39,15 +39,15 @@ using namespace std;
 enum SEGMENTED { DONT_KNOW, SEG_PLUS, SEG_MINUS, UNSEG_TOO_SHORT, UNSEG_STRAND_NOT_CONSISTENT, 
 		 UNSEG_TOO_FEW_ZERO,  UNSEG_TOO_FEW_V, UNSEG_TOO_FEW_J, 
 		 UNSEG_BAD_DELTA_MIN, UNSEG_BAD_DELTA_MAX, UNSEG_AMBIGUOUS, UNSEG_NOISY,
+		 UNSEG_TOO_SHORT_FOR_WINDOW,
 		 TOTAL_SEG_AND_WINDOW, 
-		 TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW,
 		 STATS_SIZE } ;
 const char* const segmented_mesg[] = { "?", "SEG_+", "SEG_-", "UNSEG too short", "UNSEG strand",  
 				       "UNSEG too few (0)", "UNSEG too few V", "UNSEG too few J",
 				       "UNSEG < delta_min", "UNSEG > delta_max", "UNSEG ambiguous",
                                        "UNSEG noisy",
-                                       "= SEG, with window",
-                                       "= SEG, no window",
+                                       "UNSEG too short w",
+                                       "SEG",
                                       } ;
 
 class Segmenter {

algo/core/windowExtractor.cpp

@@ -54,7 +54,7 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
         stats[TOTAL_SEG_AND_WINDOW].insert(read_length) ;
         windowsStorage->add(junc, reads->getSequence(), seg->getSegmentationStatus(), seg->segmented_germline);
       } else {
-        stats[TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW].insert(read_length) ;
+        stats[UNSEG_TOO_SHORT_FOR_WINDOW].insert(read_length) ;
       }
 
       if (out_segmented) {

algo/vidjil.cpp

@@ -966,7 +966,7 @@ int main (int argc, char **argv)
     ostringstream stream_segmentation_info;
 
     int nb_segmented_including_too_short = we.getNbSegmented(TOTAL_SEG_AND_WINDOW) 
-      + we.getNbSegmented(TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW);
+      + we.getNbSegmented(UNSEG_TOO_SHORT_FOR_WINDOW);
 
     stream_segmentation_info << "  ==> segmented " << nb_segmented_including_too_short << " reads"
 	<< " (" << setprecision(3) << 100 * (float) nb_segmented_including_too_short / nb_total_reads << "%)"