Adds citation information and gives warning if quality scores are truncated

Author: nadiadavidson

LICENSE

@@ -19,3 +19,7 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
+
+We also ask that you cite this software and its corresponding publication:
+https://doi.org/10.1093/bioinformatics/btae102, in papers where you made
+use of it for any part of the data analysis.

flexiplex.c++

@@ -25,7 +25,7 @@ using namespace std;
 
 // Append .1 to version for dev code, remove for release
 // e.g. 1.00.1 (dev) goes to 1.01 (release)
-const static string VERSION="1.02.1"; 
+const static string VERSION="1.02.2"; 
 
 struct PredefinedStruct {
   string description;
@@ -95,7 +95,11 @@ void print_usage(){
   }
   cerr << "\n     -h     Print this usage information.\n\n";
   cerr << "Have a different barcode scheme you would like Flexiplex to work with? Post a request at:\n" ;
-  cerr << "https://github.com/DavidsonGroup/flexiplex/issues\n" ;
+  cerr << "https://github.com/DavidsonGroup/flexiplex/issues\n\n" ;
+
+  cerr << "If you use Flexiplex in your research, please cite our paper:\n" ;
+  cerr << "O. Cheng et al., Flexiplex: a versatile demultiplexer and search tool for omics data, Bioinformatics, Volume 40, Issue 3, 2024 \n";
+
   cerr << endl;
 }
 
@@ -431,6 +435,7 @@ Barcode get_barcode(string & seq,
 
 //search a read for one or more barcodes (parent function that calls get_barcode)
 vector<Barcode> big_barcode_search(string & sequence, unordered_set<string> & known_barcodes, int max_flank_editd, int max_editd, const std::vector<std::pair<std::string, std::string>> &search_pattern) {
+
   vector<Barcode> return_vec; //vector of all the barcodes found
 
   //search for barcode
@@ -449,8 +454,8 @@ vector<Barcode> big_barcode_search(string & sequence, unordered_set<string> & kn
     masked_res=big_barcode_search(masked_sequence,known_barcodes,max_flank_editd,max_editd, search_pattern); //,ss);
     return_vec.insert(return_vec.end(),masked_res.begin(),masked_res.end()); //add to result
   }
-    
   return(return_vec);
+    
 }
 
 // utility function to check true/false input options
@@ -531,6 +536,10 @@ void print_read(string read_id, string read, string qual,
       string qual_new = ""; // don't trim the quality scores if it's a fasta file
 
       if (qual != "") {
+	if(qual.length()!=read_length){
+	  cerr << "WARNING: sequence and quality lengths diff for read: " << read_id << ". Ignoring read." << endl;
+	  return;
+	}
         qual_new = qual.substr(read_start, read_length);
       }
       string read_new = read.substr(read_start, read_length);
@@ -572,8 +581,8 @@ void search_read(vector<SearchResult> & reads, unordered_set<string> & known_bar
     //forward search
     auto forward_reads = big_barcode_search(
       reads[r].line,
-			known_barcodes,
-			flank_edit_distance,
+      known_barcodes,
+      flank_edit_distance,
       edit_distance,
       search_pattern
     );
@@ -585,10 +594,10 @@ void search_read(vector<SearchResult> & reads, unordered_set<string> & known_bar
     //Check the reverse compliment of the read
     auto reverse_reads = big_barcode_search(
         reads[r].rev_line,
-					   known_barcodes,
-					   flank_edit_distance,
-					   edit_distance,
-             search_pattern
+	known_barcodes,
+	flank_edit_distance,
+	edit_distance,
+        search_pattern
     );
 
     reads[r].vec_bc_for = forward_reads;
@@ -607,7 +616,7 @@ int main(int argc, char **argv) {
   std::ios_base::sync_with_stdio(false);
 
   cerr << "FLEXIPLEX " << VERSION << "\n";
-
+  
   // Variables to store user options
   // Set these to their defaults
   int expected_cells = 0;      //(d)
@@ -859,7 +868,7 @@ int main(int argc, char **argv) {
         string read_id;
 
         istringstream line_stream(read_id_line);
-        line_stream >> sr.read_id;
+	line_stream >> sr.read_id;
         sr.read_id.erase(0, 1);
 
         if (!is_fastq) { // fasta (account for multi-lines per read)
@@ -978,7 +987,8 @@ int main(int argc, char **argv) {
   cerr << "Number of reads where more than one barcode was found: "
        << multi_bc_count << "\n";
   cerr << "All done!" << endl;
-
+  cerr << "If you like Flexiplex, please cite us! https://doi.org/10.1093/bioinformatics/btae102" << endl;
+  
   if (known_barcodes.size() > 0) {
     out_stat_file.close();
     return (0);