Support additional options for mGAP tracks

bimberlabinternal · Feb 3, 2025 · 3d7d48c · 3d7d48c
1 parent 59becfa
commit 3d7d48c
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java b/mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java
@@ -456,6 +456,11 @@ private Map<String, File> processTracks(VariantProcessingStepOutputImpl output,
         List<String> options = new ArrayList<>();
         options.add("--remove-unused-alternates");
 
+        options.add("--recalculate-ac");
+        options.add("--keep-original-ac");
+        options.add("--original-ac-suffix");
+        options.add(".mGAP");
+
         options.add("--sample-mapping-file");
         options.add(sampleFile.getPath());