Add option to append barcodes from another fastq file to read names

src/cta.cpp

@@ -33,6 +33,13 @@ class FASTQRecord {
     std::string comment;
     std::string sequence;
     std::string quality;
+    void append_barcode(const std::string& barcode) {
+        if (name.find(' ')!=std::string::npos) {
+                name.insert(name.find(' '), "_" + barcode);
+        } else {
+                name += "_" + barcode;
+        }
+    }
 };
 
 std::ostream& operator<<(std::ostream& os, const FASTQRecord& record) {
@@ -279,6 +286,9 @@ void print_usage() {
               << "-t|--trim-from-start\n"
               << "    Trim this number of bases from the start of each sequence. The default is zero.\n"
 
+              << "-a|--append-barcode\n"
+              << "    Append barcodes from this fastq file to the end of read names (useful for e.g. single-cell data).\n"
+
               << std::endl;
 }
 
@@ -293,6 +303,7 @@ int main(int argc, char **argv)
     long long int rc_length = 20;
     std::string input_filename1;
     std::string input_filename2;
+    std::string barcode_filename;
     std::string output_filename1;
     std::string output_filename2;
 
@@ -304,11 +315,12 @@ int main(int argc, char **argv)
         {"fudge", required_argument, NULL, 'f'},
         {"trim-from-start", required_argument, NULL, 't'},
         {"rc-length", required_argument, NULL, 'r'},
+        {"append-barcode", required_argument, NULL, 'a'},
         {0, 0, 0, 0}
     };
 
     // parse the command line arguments
-    while ((c = getopt_long(argc, argv, "d:f:t:r:vh?", long_options, &option_index)) != -1) {
+    while ((c = getopt_long(argc, argv, "d:f:t:r:a:vh?", long_options, &option_index)) != -1) {
         switch (c) {
         case 'h':
         case '?':
@@ -329,6 +341,9 @@ int main(int argc, char **argv)
         case 'r':
             rc_length = std::stoll(optarg);
             break;
+        case 'a':
+            barcode_filename = optarg;
+            break;
         case 0:
             if (long_options[option_index].flag != 0){
                 break;
@@ -369,6 +384,9 @@ int main(int argc, char **argv)
     bio::file_source input_file2(input_filename2);
     bio::stream<bio::file_source> input_stream2(input_file2);
 
+    bio::file_source barcode_file(barcode_filename);
+    bio::stream<bio::file_source> barcode_stream(barcode_file);
+
     bio::filtering_stream<bio::input> in1;
     if (is_gzipped_file(input_filename1)) {
         in1.push(bio::gzip_decompressor());
@@ -381,6 +399,12 @@ int main(int argc, char **argv)
     }
     in2.push(input_stream2);
 
+    bio::filtering_stream<bio::input> inBarcode;
+    if (!barcode_filename.empty() && is_gzipped_file(barcode_filename)) {
+        inBarcode.push(bio::gzip_decompressor());
+    }
+    inBarcode.push(barcode_stream);
+
     if (output_filename1.empty()) {
         output_filename1 = make_trimmed_filename(input_filename1);
     }
@@ -410,9 +434,16 @@ int main(int argc, char **argv)
 
     FASTQRecord record1;
     FASTQRecord record2;
+    FASTQRecord recordBarcode;
 
     while ((in1 >> record1) && (in2 >> record2)) {
         trim_pair(record1, record2, rc_length, max_edit_distance, fudge, trim_start, verbose);
+        if (!barcode_filename.empty()) {
+                inBarcode >> recordBarcode;
+                std::string barcode = recordBarcode.sequence;
+                record1.append_barcode(barcode);
+                record2.append_barcode(barcode);
+        }
         out1 << record1;
         out2 << record2;
     }