All changes commited. Error messages updated.

Author: dbeyter

fast5

@@ -618,7 +618,7 @@ void AlignmentDB::_clear_region()
 
 //added by dorukb
 bool AlignmentDB::find_event_coords_for_region_for_record(const SequenceAlignmentRecordInfo& sequence_record, 
-										const int start_pos, const int stop_pos, int& event_begin_idx, int& event_end_idx)
+										const int start_pos, const int stop_pos, int& event_begin_idx, int& event_end_idx, bool& event_mismatch)
 {
 
 	int r1 = 0, r2 = 0;
@@ -631,7 +631,7 @@ bool AlignmentDB::find_event_coords_for_region_for_record(const SequenceAlignmen
 	}
 
 	std::vector<int> event_inds_for_bases;
-	bool success = find_scrappie_events_for_basecall(sequence_record, event_inds_for_bases);
+	bool success = find_scrappie_events_for_basecall(sequence_record, event_inds_for_bases, event_mismatch);
 
 	if (success)
 	{
@@ -649,11 +649,11 @@ bool AlignmentDB::find_event_coords_for_region_for_record(const SequenceAlignmen
 
 //added by dorukb
 bool AlignmentDB::find_event_coords_for_given_read_coords(const SequenceAlignmentRecordInfo& sequence_record, 
-										const int r1, const int r2, int& event_begin_idx, int& event_end_idx) const
+										const int r1, const int r2, int& event_begin_idx, int& event_end_idx, bool& event_mismatch) const
 {
 
 	std::vector<int> event_inds_for_bases;
-	bool success = find_scrappie_events_for_basecall(sequence_record, event_inds_for_bases);
+	bool success = find_scrappie_events_for_basecall(sequence_record, event_inds_for_bases, event_mismatch);
 
 	if (success)
 	{
@@ -672,9 +672,9 @@ bool AlignmentDB::find_event_coords_for_given_read_coords(const SequenceAlignmen
 }
 
 
-bool AlignmentDB::find_scrappie_events_for_basecall(const SequenceAlignmentRecordInfo& sequence_record, std::vector<int>& event_indices_for_bases) const
+bool AlignmentDB::find_scrappie_events_for_basecall(const SequenceAlignmentRecordInfo& sequence_record, std::vector<int>& event_indices_for_bases, bool& event_mismatch) const
 {
-
+	event_mismatch = false;
 	SquiggleRead* sr;
 	if (m_squiggle_read_map.find(sequence_record.read_name) != m_squiggle_read_map.end())
 	{
@@ -687,7 +687,8 @@ bool AlignmentDB::find_scrappie_events_for_basecall(const SequenceAlignmentRecor
 		std::abort();
 	}
 
-	bool success = map_events_to_basecall(sr, event_indices_for_bases);
+	
+	bool success = map_events_to_basecall(sr, event_indices_for_bases, event_mismatch);
 	return success;
 
 }

src/alignment/nanopolish_alignment_db.cpp

@@ -128,13 +128,13 @@ class AlignmentDB
 
         //added by dorukb
         bool find_event_coords_for_region_for_record(const SequenceAlignmentRecordInfo& sequence_record, 
-                                        const int start_pos, const int stop_pos, int& event_begin_idx, int& event_end_idx);
+                                        const int start_pos, const int stop_pos, int& event_begin_idx, int& event_end_idx, bool& event_mismatch);
 
 
 
         //added by dorukb
         bool find_event_coords_for_given_read_coords(const SequenceAlignmentRecordInfo& sequence_record, 
-                                        const int r1, const int r2, int& event_begin_idx, int& event_end_idx) const;
+                                        const int r1, const int r2, int& event_begin_idx, int& event_end_idx, bool& event_mismatch) const;
 
 
         std::vector<HMMInputData> get_events_aligned_to(const std::string& contig, int position) const;
@@ -187,7 +187,7 @@ class AlignmentDB
                                                 const std::string& sequence_bam) const;
 
 
-        bool find_scrappie_events_for_basecall(const SequenceAlignmentRecordInfo& sequence_record, std::vector<int>& event_indices_for_bases) const;
+        bool find_scrappie_events_for_basecall(const SequenceAlignmentRecordInfo& sequence_record, std::vector<int>& event_indices_for_bases, bool& event_mismatch) const;
 
 
 

src/alignment/nanopolish_alignment_db.h

@@ -31,7 +31,7 @@ static std::map< std::string, std::function<int(int, char**)> > programs = {
     {"help",        print_usage},
     {"--help",      print_usage},
     {"--version",   print_version},
-    //{"index",       index_main},
+    {"index",       index_main},
     //{"extract",     extract_main},
     //{"eventalign",  eventalign_main},
     //{"getmodel",    getmodel_main},