[FIX] ignore reference sequence on negative strand in maf file when created for annotation with mmseqs (sequences will already be in reverse complement and shortened depending on phase)

Author: cpockrandt

src/parallel_file_reader.hpp

@@ -427,7 +427,7 @@ class parallel_maf_reader
     // in practice aln.ids will already be set and only
     // if only \n is at the end of the range for a thread, don't process it
     // if "\na" isn at the end of the range for a thread, process it
-    bool get_next_alignment(alignment_t & aln, const unsigned job_id, std::vector<bool> * species_seen_in_alignment = NULL)
+    bool get_next_alignment(alignment_t & aln, const unsigned job_id, std::vector<bool> * species_seen_in_alignment = NULL, const bool single_block_scoring = false)
     {
         #pragma omp atomic
         total_bytes_processed += bytes_processing[job_id];
@@ -536,7 +536,7 @@ class parallel_maf_reader
 
                         // printf("First alignment block (chrom: %s, start: %lld, cum len: %lld)\n", aln.chrom.c_str(), aln.start_pos, prev_cumulative_len_wo_ref_gaps);
 
-                        if (ref_strand != '+')
+                        if (ref_strand != '+' && !single_block_scoring)
                         {
                             printf(OUT_ERROR "Reference sequence is not on the + strand (%s.%s at position %" PRIu64 ")!\n" OUT_RESET, id, chrom, start_pos);
                             exit(-1);
@@ -574,7 +574,7 @@ class parallel_maf_reader
                             printf(OUT_ERROR "Encountered an alignment block that didn't start with the reference species: %s.%s at position %" PRIu64 "!\n" OUT_RESET, id, chrom, start_pos);
                             exit(1);
                         }
-                        if (ref_strand != '+')
+                        if (ref_strand != '+' && !single_block_scoring)
                         {
                             printf(OUT_ERROR "Reference sequence is not on the + strand (%s.%s at position %" PRIu64 ")!\n" OUT_RESET, id, chrom, start_pos);
                             exit(-1);

src/phylocsf++score_msa.hpp

@@ -99,7 +99,7 @@ void run_scoring_msa(const std::string & alignment_path, const Model & model, co
         alignment_t & aln = alignments[thread_id];
         std::vector<scoring_result> & results = all_results[job_id];
 
-        while (maf_rd.get_next_alignment(aln, job_id))
+        while (maf_rd.get_next_alignment(aln, job_id, NULL, true))
         {
             maf_rd.print_progress();