Ambiguous within thread gets only reset for better alignments

bismark

@@ -3039,10 +3039,14 @@ sub check_bowtie_results_single_end_bowtie2{
 	      # 19 07 2016: changed this to >= so that equally good alignments are also added. Ambiguous alignments from different threads will be identified later on
 	      $best_AS_so_far = $alignment_score;
 	      $overwrite++;
-	      # warn "Found better alignment score ($alignment_score), setting \$best_AS_so_far to $best_AS_so_far\n";
-	      # resetting the ambiguous within thread memory (if applicable at all)
-	      # warn "Resetting amb within thread value to 0\n";
-	      $amb_same_thread = 0;
+	      # warn "Found better or equal alignment score ($alignment_score), setting \$best_AS_so_far to $best_AS_so_far\n";
+
+	      # resetting the ambiguous within thread memory (if applicable at all) only if the current alignment is really better than the previous one.
+	      # 22 07 2016: ambiguous score within same read only resets if the current alignment is really better than the previous one
+	      if ($alignment_score > $best_AS_so_far){
+		  # warn "Resetting amb within thread value to 0\n";
+		  $amb_same_thread = 0;
+	      }
 
 	      if ($ambig_bam){ # also setting a new first_ambig_alignment
 		  $first_ambig_alignment = $fhs[$index]->{last_line};
@@ -3051,7 +3055,7 @@ sub check_bowtie_results_single_end_bowtie2{
 	      }
 	  }
 	  else{
-	      # warn "Current alignment (AS $alignment_score) isn't better than the best so far ($best_AS_so_far). Not changing anything\n";
+	      warn "Current alignment (AS $alignment_score) isn't better than the best so far ($best_AS_so_far). Not changing anything\n";
 	  }
       }
 
@@ -3073,6 +3077,7 @@ sub check_bowtie_results_single_end_bowtie2{
 	      else{
 		  # warn "This read has a worse alignments score than the best alignment so far and will be ignored even though it is ambiguous in itself\n";
 	      }
+
 	      ### if there is a better alignment later on -> fine. If not, the read will get booted altogether
 
 	      ## need to read and discard all additional ambiguous reads until we reach the next sequence
@@ -3980,10 +3985,14 @@ sub check_bowtie_results_paired_ends_bowtie2{
 		# 19 07 2016 Changed to >= so that equally good alignments to different positions get added as well. Ambiguous alignments are identified and removed later.
 		$best_AS_so_far = $sum_of_alignment_scores_1;
 		$overwrite = 1;
-		# warn "Found better sum of alignment scores ($sum_of_alignment_scores_1), setting \$best_AS_so_far to $best_AS_so_far\n";
-		# resetting the ambiguous within thread memory (if applicable at all)
-		# warn "Resetting amb within thread value to 0\n";
-		$amb_same_thread = 0;
+
+		# warn "Found better or equal sum of alignment scores ($sum_of_alignment_scores_1), setting \$best_AS_so_far to $best_AS_so_far\n";
+		# resetting the ambiguous within thread memory (if applicable at all) only if the current alignment is really better than the previous one.
+		# 22 07 2016: ambiguous score within same read only resets if the current alignment is really better than the previous one
+		if ($sum_of_alignment_scores_1 > $best_AS_so_far){
+		    # warn "Resetting amb within thread value to 0\n";
+		    $amb_same_thread = 0;
+		}
 
 		if ($ambig_bam){ # also setting a new first_ambig_alignment
 		    # Read 1
@@ -10207,6 +10216,6 @@ Bismark SAM OUTPUT (default):
 Each read of paired-end alignments is written out in a separate line in the above format.
 
 
-Last edited on 20 July 2016
+Last edited on 22 July 2016
 HOW_TO
 }