From 5395d75189f8e0445f5f40a44f2151c2478a6716 Mon Sep 17 00:00:00 2001
From: Ilya Soifer <ilya.soifer@ultimagen.com>
Date: Wed, 24 May 2023 22:14:24 +0300
Subject: [PATCH] Fixed tests

---
 .../utils/read/FlowBasedReadUtils.java        | 38 +++++++++++++------
 .../read/FlowBasedReadUtilsUnitTest.java      | 12 +++++-
 2 files changed, 37 insertions(+), 13 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtils.java
index f5b251393e4..d7a7a76faaf 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtils.java
@@ -15,8 +15,15 @@
 import java.util.LinkedHashMap;
 import java.util.Map;
 
+
 /**
- * utility class for flow based read
+ * Utility class for working with flow-based reads
+ *
+ * The main member static class is {@code ReadGroupInfo} that contains methods that allow
+ * working with headers of flow based reads and extracting the flow order and the maximal hmer class called.
+ * It also contains methods to check how the read was clipped ({@code readEndMarkedUnclipped}, {@code readEndMarkedUncertain})
+ * Lastly, {@code FlowBasedReadUtils.isFlowPlatform} is **the** function to determine if the data are flow-based
+ *
  */
 public class FlowBasedReadUtils {
 
@@ -37,20 +44,19 @@ public ReadGroupInfo(final SAMReadGroupRecord readGroup) {
                 isFlowPlatform = false;
             } else if (NGSPlatform.fromReadGroupPL(readGroup.getPlatform())==NGSPlatform.UNKNOWN){
                 isFlowPlatform = false;
-            } else {
-                //old Ultima data can have PLATFORM==LS454
-                // we require also FO field to consider ReadGroup to come from the flow
-                boolean tmp = (NGSPlatform.fromReadGroupPL(readGroup.getPlatform()) == NGSPlatform.LS454) ||
-                        (NGSPlatform.fromReadGroupPL(readGroup.getPlatform()) == NGSPlatform.ULTIMA);
-                tmp = tmp & (readGroup!=null);
-                tmp = tmp  & (readGroup.getFlowOrder()!=null);
-                isFlowPlatform = tmp;
-
-                //in addition validate that the ultima data has FO tag, otherwise break
-                if ((NGSPlatform.fromReadGroupPL(readGroup.getPlatform()) == NGSPlatform.ULTIMA) & (!isFlowPlatform)){
+            } else if (NGSPlatform.fromReadGroupPL(readGroup.getPlatform()) == NGSPlatform.LS454) {
+                //old Ultima data can have PLATFORM==LS454 and not have FO tag
+                isFlowPlatform = true;
+            } else if (NGSPlatform.fromReadGroupPL(readGroup.getPlatform()) == NGSPlatform.ULTIMA){
+                if (readGroup.getFlowOrder()!=null) {
+                    isFlowPlatform = true;
+                } else {
                     throw new RuntimeException("Malformed Ultima read group identified, aborting: " + readGroup);
                 }
+            } else {
+                isFlowPlatform = false;
             }
+
             if (isFlowPlatform) {
                 this.flowOrder = readGroup.getFlowOrder();
                 String mc = readGroup.getAttribute(FlowBasedRead.MAX_CLASS_READ_GROUP_TAG);
@@ -154,6 +160,14 @@ public static boolean hasFlowTags(final SAMRecord rec) {
 
     }
 
+    /**
+     *
+     * This is the function to run if you want to ask if the data are flow-based
+     *
+     * @param hdr - file header
+     * @param read - the read
+     * @return true if the read is flow-based
+     */
     public static boolean isFlowPlatform(final SAMFileHeader hdr, final GATKRead read) {
         if (!hasFlowTags(read)){
             return false;
diff --git a/src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtilsUnitTest.java
index ec935c1f68e..b249b21461b 100644
--- a/src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtilsUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtilsUnitTest.java
@@ -97,7 +97,7 @@ Object[][] getIsFlowPlatformInputs() {
         rg3.setPlatform("LS454");
         read3.setReadGroup("rg3");
         hdr.addReadGroup(rg3);
-        tests.add(new Object[]{hdr, read3, false});
+        tests.add(new Object[]{hdr, read3, true});
 
         GATKRead read4 = makeRead(new byte[]{'T','A','G','C','G','A'}, false);
         read4.setAttribute("tp",new byte[6]);
@@ -108,6 +108,16 @@ Object[][] getIsFlowPlatformInputs() {
         hdr.addReadGroup(rg4);
         tests.add(new Object[]{hdr, read4, true});
 
+        GATKRead read5 = makeRead(new byte[]{'T','A','G','C','G','A'}, false);
+        read5.setAttribute("tp",new byte[6]);
+        SAMReadGroupRecord rg5 = new SAMReadGroupRecord("rg5");
+        rg5.setPlatform("LS454");
+        rg5.setAttribute("FO","TGCATGCA");
+        read5.setReadGroup("rg5");
+        hdr.addReadGroup(rg5);
+        tests.add(new Object[]{hdr, read5, true});
+
+
         return tests.toArray(new Object[][]{});
     }