From 3d7d48c56ff2ba883e33799a16efed1669f23e36 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Sun, 2 Feb 2025 18:04:43 -0800
Subject: [PATCH] Support additional options for mGAP tracks

---
 .../src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java b/mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java
index c1d89037..ace73b8e 100644
--- 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());