now prints alignments to contigs which do not appear in the vcf as th…

…ey were (previously the RNAME is empty for such contigs); also prints the contigs in the header of lifted sam

liftover.cpp

@@ -143,6 +143,12 @@ void lift_run(lift_opts args) {
     for (auto i = 0; i < contig_names.size(); ++i) {
         fprintf(out_sam_fp, "@SQ\tSN:%s\tLN:%ld\n", contig_names[i].data(), contig_reflens[i]);
     }
+    for (auto i = 0; i < hdr->n_targets; i++){
+        // if a contig is not found in vcf/lft, print it as it was before liftover
+        if (std::find(contig_names.begin(), contig_names.end(), hdr->target_name[i]) == contig_names.end()){
+            fprintf(out_sam_fp, "@SQ\tSN:%s\tLN:%u\n", hdr->target_name[i], hdr->target_len[i]);
+        }
+    }
     /* This is only supported in the latest dev release of htslib as of July 22. 
      * add back in at next htslib release
     kstring_t s = KS_INITIALIZE;
@@ -278,7 +284,7 @@ int main(int argc, char** argv) {
         exit(1);
     }
     if (args.haplotype != "0" && args.haplotype != "1"){
-        fprintf(stderr, "invalid haplotype %s\n", args.haplotype);
+        fprintf(stderr, "invalid haplotype %s\n", args.haplotype.c_str());
         exit(1);
     }
     if (!strcmp(argv[optind], "lift")) {

liftover.hpp

@@ -368,7 +368,10 @@ class LiftMap {
     std::string get_other_name(std::string n) {
         if (name_map.find(n) != name_map.end()) {
             return name_map[n];
-        } else return "";
+        }
+        // return original name if mapping is not available
+        else
+            return n;
     }
 
     // converts CIGAR string of s2 alignment to corresponding CIGAR string for the s1 alignment