add option to output haplotypes afte vg rna

src/subcommand/rna_main.cpp

@@ -54,6 +54,7 @@ void help_rna(char** argv) {
          << "\nOutput options:" << endl
 
          << "    -b, --write-gbwt FILE      write pantranscriptome transcript paths as GBWT index file" << endl
+         << "    -v, --write-hap-gbwt FILE  write input haplotypes as a GBWT with node IDs matching the output graph" << endl
          << "    -f, --write-fasta FILE     write pantranscriptome transcript sequences as fasta file" << endl
          << "    -i, --write-info FILE      write pantranscriptome transcript info table as tsv file" << endl
          << "    -q, --out-exclude-ref      exclude reference transcripts from pantranscriptome output" << endl
@@ -88,6 +89,7 @@ int32_t main_rna(int32_t argc, char** argv) {
     bool gbwt_add_bidirectional = false;
     string fasta_out_filename = "";
     string info_out_filename = "";
+    string hap_gbwt_out_filename = "";
     int32_t num_threads = 1;
     bool show_progress = false;
 
@@ -110,8 +112,9 @@ int32_t main_rna(int32_t argc, char** argv) {
                 {"remove-non-gene",  no_argument, 0, 'd'},
                 {"do-not-sort",  no_argument, 0, 'o'},
                 {"add-ref-paths",  no_argument, 0, 'r'},
-                {"add-hap-paths",  no_argument, 0, 'a'},      
+                {"add-hap-paths",  no_argument, 0, 'a'},
                 {"write-gbwt",  required_argument, 0, 'b'},
+                {"write-hap-gbwt",  required_argument, 0, 'v'},
                 {"write-fasta",  required_argument, 0, 'f'},
                 {"write-info",  required_argument, 0, 'i'},
                 {"out-ref-paths",  no_argument, 0, 'u'},
@@ -124,7 +127,7 @@ int32_t main_rna(int32_t argc, char** argv) {
             };
 
         int32_t option_index = 0;
-        c = getopt_long(argc, argv, "n:m:y:s:l:zjec:k:dorab:f:i:uqgt:ph?", long_options, &option_index);
+        c = getopt_long(argc, argv, "n:m:y:s:l:zjec:k:dorab:v:f:i:uqgt:ph?", long_options, &option_index);
 
         /* Detect the end of the options. */
         if (c == -1)
@@ -188,10 +191,14 @@ int32_t main_rna(int32_t argc, char** argv) {
         case 'a':
             add_projected_transcript_paths = true;
             break;
-
+                
         case 'b':
             gbwt_out_filename = optarg;
             break;
+
+        case 'v':
+            hap_gbwt_out_filename = optarg;
+            break;
 
         case 'f':
             fasta_out_filename = optarg;
@@ -486,6 +493,19 @@ int32_t main_rna(int32_t argc, char** argv) {
         gbwt_builder.finish();
         save_gbwt(gbwt_builder.index, gbwt_out_filename);
     }
+
+    // Write a haplotype GBWT with node IDs updated to match the spliced graph.
+    if (!hap_gbwt_out_filename.empty()) {
+        if (!haplotype_index.get()) {
+            cerr << "[vg rna] Warning: not saving updated haplotypes to " << hap_gbwt_out_filename << " because haplotypes were not provided as input" << endl;
+        }
+        else {
+            ofstream hap_gbwt_ostream;
+            hap_gbwt_ostream.open(hap_gbwt_out_filename);
+
+            haplotype_index->serialize(hap_gbwt_ostream);
+        }
+    }
 
     // Write transcript sequences in transcriptome as fasta file.
     if (!fasta_out_filename.empty()) {
@@ -496,7 +516,7 @@ int32_t main_rna(int32_t argc, char** argv) {
         transcriptome.write_transcript_sequences(&fasta_ostream, exclude_reference_transcripts);
 
         fasta_ostream.close();
-    }    
+    }
 
     // Write transcript info in transcriptome as tsv file.
     if (!info_out_filename.empty()) {