Fix issue caused by unpaired reads. Reads that are neither the 1st no…

…r the 2nd read caused an adapter trimming assertion to fail

src/adapter_trimmer.cpp

@@ -148,7 +148,7 @@ void AdapterTrimmer::trim_adapters(BamAlignment& aln){
 
   double start_time = clock(); // Start the clock
   int64_t num_trim;
-  if (aln.IsFirstMate()){
+  if (aln.IsFirstMate() || (!aln.IsPaired())){
     if (aln.IsReverseStrand())
       num_trim = trim_five_prime(aln, r1_rc_adapters_);
     else
@@ -168,8 +168,11 @@ void AdapterTrimmer::trim_adapters(BamAlignment& aln){
     locus_r2_trimmed_reads_ += (num_trim > 0 ? 1 : 0);
     locus_r2_total_reads_++;
   }
-  else
+  else {
+    printErrorAndDie(aln.Name());
     assert(false);
+  }
+
   locus_trimming_time_ += (clock() - start_time)/CLOCKS_PER_SEC; // Turn off the clock
 }
 

src/bam_processor.cpp

@@ -189,6 +189,10 @@ void BamProcessor::read_and_filter_reads(BamCramMultiReader& reader, const std::
   std::string file_label = "0_";
 
   while (reader.GetNextAlignment(alignment)){
+    // Discard reads where the 1st/2nd mate info isn't clear
+    if (alignment.IsPaired() && (!alignment.IsFirstMate() && !alignment.IsSecondMate()))
+      continue;
+
     // Discard reads that don't overlap the STR region and whose mate pair has no chance of overlapping the region
     if (alignment.Position() > region_group.stop() || alignment.GetEndPosition() < region_group.start()){
       if (!alignment.IsPaired() || alignment.MatePosition() == alignment.Position())