Introduce compareCoordinatesAndStrand function

biod · Feb 23, 2017 · be19909 · be19909
1 parent ccd2741
commit be19909
Show file tree

Hide file tree

Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/BioD b/BioD
diff --git a/sambamba/merge.d b/sambamba/merge.d
@@ -386,7 +386,7 @@ int merge_main(string[] args) {
                         writer.writeRecord(read);
                     break;
                 case SortingOrder.coordinate:
-                    foreach (read; nWayUnion!compareCoordinates(modifiedranges))
+                    foreach (read; nWayUnion!compareCoordinatesAndStrand(modifiedranges))
                         writer.writeRecord(read);
                     break;
                 default: assert(0);

diff --git a/sambamba/sort.d b/sambamba/sort.d
@@ -217,7 +217,7 @@ class Sorter {
         } else if (natural_sort) {
             mergeSort!(mixedCompareReadNames, false)(chunk, task_pool, tmp);
         } else {
-            mergeSort!(compareCoordinates, false)(chunk, task_pool, tmp);
+            mergeSort!(compareCoordinatesAndStrand, false)(chunk, task_pool, tmp);
         }
         version (development) {
         stderr.writeln("Finished sorting of chunk #", n, " in ", sw.peek().seconds, "s");
@@ -266,7 +266,7 @@ class Sorter {
         else if (natural_sort)
             mergeSortedChunks!mixedCompareReadNames();
         else
-            mergeSortedChunks!compareCoordinates();
+            mergeSortedChunks!compareCoordinatesAndStrand();
     }
 
     private void createHeader() {