core/windowExtractor.{h,cpp}, vidjil.cpp: W09 when interrupted during first pass

algo/core/windowExtractor.cpp

@@ -18,7 +18,8 @@ WindowsStorage *WindowExtractor::extract(OnlineBioReader *reads,
                                          map<string, string> &windows_labels, bool only_labeled_windows,
                                          bool keep_unsegmented_as_clone,
                                          double nb_expected, int nb_reads_for_evalue,
-                                         VirtualReadScore *scorer) {
+                                         VirtualReadScore *scorer,
+                                         SampleOutput *output) {
   init_stats();
 
   WindowsStorage *windowsStorage = new WindowsStorage(windows_labels);
@@ -34,7 +35,9 @@ WindowsStorage *WindowExtractor::extract(OnlineBioReader *reads,
 
     if (global_interrupted)
     {
-      cout << WARNING_STRING << "Interrupted after processing " << nb_reads << " reads" << endl ;
+      string msg = "Interrupted after processing " + string_of_int(nb_reads) + " reads" ;
+      if (output) output->add_warning("W09", msg, LEVEL_WARN);
+      cout << WARNING_STRING << msg << endl ;
       break;
     }
 

algo/core/windowExtractor.h

@@ -12,6 +12,7 @@
 #include "read_storage.h"
 #include "bioreader.hpp"
 #include "read_score.h"
+#include "output.h"
 
 #define NB_BINS_CLONES 10
 #define MAX_VALUE_BINS_CLONES 1000
@@ -53,6 +54,7 @@ class WindowExtractor {
    * @param nb_expected: maximal e-value of the segmentation
    * @param nb_reads_for_evalue: number of reads, used for e-value computation. Can be approximate or faked.
    * @param scorer: how reads are scored (only the best ones are keeped for large clones)
+   * @param output: global output, used here for warnings
    * @return a pointer to a WindowsStorage that will contain all the windows.
    *         It is a pointer so that the WindowsStorage is not duplicated.
    * @post Statistics on segmentation will be provided through the getSegmentationStats() methods
@@ -63,7 +65,8 @@ class WindowExtractor {
                           map<string, string> &windows_labels, bool only_labeled_windows=false,
                           bool keep_unsegmented_as_clone=false,
                           double nb_expected = THRESHOLD_NB_EXPECTED, int nb_reads_for_evalue = 1,
-                          VirtualReadScore *scorer = &DEFAULT_READ_SCORE);
+                          VirtualReadScore *scorer = &DEFAULT_READ_SCORE,
+                          SampleOutput *output = NULL);
 
   /**
    * @return the average length of sequences whose segmentation has been classified as seg

algo/vidjil.cpp

@@ -1133,7 +1133,7 @@ int main (int argc, char **argv)
                                                 windows_labels, only_labeled_windows,
                                                 keep_unsegmented_as_clone,
                                                 expected_value_kmer, nb_reads_for_evalue,
-                                                readScorer);
+                                                readScorer, &output);
     windowsStorage->setIdToAll();
     size_t nb_total_reads = we.getNbReads();