From f984442fac47acaac7cb06a7f64296d100babf29 Mon Sep 17 00:00:00 2001
From: Ilya Soifer <ilya.soifer@ultimagen.com>
Date: Tue, 24 Jan 2023 18:21:59 +0200
Subject: [PATCH 1/3] Fixed my misunderstanding of t0 format

---
 .../broadinstitute/hellbender/utils/read/FlowBasedRead.java   | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java b/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java
index f00e9a3edcc..706e48d0d6b 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java
@@ -363,9 +363,7 @@ private void parseZeroQuals(final double[] probs, final int flowIdx, final int q
         if ((qualOfs == 0) | (qualOfs==probs.length)){ // do not report zero error probability on the edge of the read
             return;
         }
-        if ((probs[qualOfs-1])==(probs[qualOfs])){
-            flowMatrix[1][flowIdx] = Math.max(flowMatrix[1][flowIdx], Math.max(probs[qualOfs-1],probs[qualOfs]));
-        }
+        flowMatrix[1][flowIdx] = Math.max(flowMatrix[1][flowIdx], Math.min(probs[qualOfs-1],probs[qualOfs]));
     }
 
     public String getFlowOrder() {

From 1b1e6017d49b4e0d67134d4f3bdb75f21b3c58c7 Mon Sep 17 00:00:00 2001
From: Ilya Soifer <ilya.soifer@ultimagen.com>
Date: Sun, 5 Feb 2023 12:08:07 +0200
Subject: [PATCH 2/3] [BIOIN-882] Updated tests

---
 .../utils/read/FlowBasedReadUnitTest.java     | 73 ++++++++++++++-----
 .../reads/outputs/sample.t0.11.matrix.txt     |  8 +-
 .../reads/outputs/sample.t0.15.matrix.txt     | 20 ++---
 .../reads/outputs/sample.t0.17.matrix.txt     | 46 ++++++------
 .../reads/outputs/sample.t0.23.matrix.txt     |  4 +-
 .../flow/reads/outputs/sample.t0.3.matrix.txt | 12 +--
 .../flow/reads/outputs/sample.t0.5.matrix.txt | 26 +++----
 7 files changed, 112 insertions(+), 77 deletions(-)

diff --git a/src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUnitTest.java
index 8659f78f3f0..69503f49d2f 100644
--- a/src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUnitTest.java
@@ -20,6 +20,12 @@
 
 public class FlowBasedReadUnitTest extends GATKBaseTest {
 
+    // If true, update the expected outputs in tests that assert an exact match vs. prior output,
+    // instead of actually running the tests. Can be used with "./gradlew test -Dtest.single=HaplotypeCallerIntegrationTest"
+    // to update all of the exact-match tests at once. After you do this, you should look at the
+    // diffs in the new expected outputs in git to confirm that they are consistent with expectations.
+    public static final boolean UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS = false;
+
     @Test
     void testBAMFormatParsing() throws Exception{
         final String    testResourceDir = publicTestDir + "org/broadinstitute/hellbender/utils/read/flow/reads/";
@@ -38,23 +44,35 @@ void testBAMFormatParsing() throws Exception{
         for ( sr = reader.iterator(), curRead = 0 ; sr.hasNext(); curRead++) {
             final FlowBasedRead fbr = new FlowBasedRead(sr.next(),flowOrder, 12, fbargs);
             fbr.applyAlignment();
-            Assert.assertEquals(fbr.totalKeyBases(), fbr.seqLength());
-
-            try (FileWriter fos = new FileWriter(tempOutputDir + "/" + curRead + ".key.txt")) {
-                fbr.writeKey(fos);
-            }
-
 
             String expectedFile = outputDir + "sample." + curRead + ".key.txt";
-            IntegrationTestSpec.assertEqualTextFiles(new File(tempOutputDir + "/" + curRead + ".key.txt"), new File(expectedFile));
-            try (FileWriter fos = new FileWriter(tempOutputDir + "/" + curRead + ".matrix.txt")){
-                fbr.writeMatrix(fos);
+            if (!UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS) {
+                Assert.assertEquals(fbr.totalKeyBases(), fbr.seqLength());
+                try (FileWriter fos = new FileWriter(tempOutputDir + "/" + curRead + ".key.txt")) {
+                    fbr.writeKey(fos);
+                }
+                IntegrationTestSpec.assertEqualTextFiles(new File(tempOutputDir + "/" + curRead + ".key.txt"), new File(expectedFile));
+            } else {
+                try (FileWriter fos = new FileWriter(expectedFile)) {
+                    fbr.writeKey(fos);
+                }
             }
             expectedFile = outputDir + "sample." + curRead + ".matrix.txt";
-            IntegrationTestSpec.assertEqualTextFiles(new File(tempOutputDir + "/" + curRead + ".matrix.txt"), new File(expectedFile));
+
+            if (!UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS) {
+                try (FileWriter fos = new FileWriter(tempOutputDir + "/" + curRead + ".matrix.txt")) {
+                    fbr.writeMatrix(fos);
+                }
+                IntegrationTestSpec.assertEqualTextFiles(new File(tempOutputDir + "/" + curRead + ".matrix.txt"), new File(expectedFile));
+            } else {
+                try (FileWriter fos = new FileWriter(expectedFile)) {
+                    fbr.writeMatrix(fos);
+                }
+            }
         }
     }
 
+
     @Test
     void testBAMFormatParsingWithT0() throws Exception{
         final String    testResourceDir = publicTestDir + "org/broadinstitute/hellbender/utils/read/flow/reads/";
@@ -73,20 +91,33 @@ void testBAMFormatParsingWithT0() throws Exception{
         for ( sr = reader.iterator(), curRead = 0 ; sr.hasNext(); curRead++) {
             final FlowBasedRead fbr = new FlowBasedRead(sr.next(),flowOrder, 12, fbargs);
             fbr.applyAlignment();
-            Assert.assertEquals(fbr.totalKeyBases(), fbr.seqLength());
+            String expectedFile = outputDir + "sample.t0." + curRead + ".key.txt";
 
-            try (FileWriter fos = new FileWriter(tempOutputDir + "/" + curRead + ".key.txt")) {
-                fbr.writeKey(fos);
+            if ( !UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ) {
+                Assert.assertEquals(fbr.totalKeyBases(), fbr.seqLength());
+                try (FileWriter fos = new FileWriter(tempOutputDir + "/" + curRead + ".key.txt")) {
+                    fbr.writeKey(fos);
+                }
+                IntegrationTestSpec.assertEqualTextFiles(new File(tempOutputDir + "/" + curRead + ".key.txt"), new File(expectedFile));
+            } else {
+                try (FileWriter fos = new FileWriter( expectedFile )) {
+                    fbr.writeKey(fos);
+                }
             }
 
+            expectedFile = outputDir + "sample.t0." + curRead + ".matrix.txt";
+
+            if (!UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS) {
+                try (FileWriter fos = new FileWriter(tempOutputDir + "/" + curRead + ".matrix.txt")) {
+                    fbr.writeMatrix(fos);
+                }
+                IntegrationTestSpec.assertEqualTextFiles(new File(tempOutputDir + "/" + curRead + ".matrix.txt"), new File(expectedFile));
+            } else {
+                try (FileWriter fos = new FileWriter(expectedFile)) {
+                    fbr.writeMatrix(fos);
+                }
 
-            String expectedFile = outputDir + "sample.t0." + curRead + ".key.txt";
-            IntegrationTestSpec.assertEqualTextFiles(new File(tempOutputDir + "/" + curRead + ".key.txt"), new File(expectedFile));
-            try (FileWriter fos = new FileWriter(tempOutputDir + "/" + curRead + ".matrix.txt")){
-                fbr.writeMatrix(fos);
             }
-            expectedFile = outputDir + "sample.t0." + curRead + ".matrix.txt";
-            IntegrationTestSpec.assertEqualTextFiles(new File(tempOutputDir + "/" + curRead + ".matrix.txt"), new File(expectedFile));
         }
     }
 
@@ -165,5 +196,9 @@ public void testArtificialFlowBasedReadConstruction() {
         new FlowBasedRead(read, FlowBasedRead.DEFAULT_FLOW_ORDER, FlowBasedRead.MAX_CLASS, new FlowBasedArgumentCollection());
     }
 
+    @Test
+    public void assertThatExpectedOutputUpdateToggleIsDisabled() {
+        Assert.assertFalse(UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS, "The toggle to update expected outputs should not be left enabled");
+    }
 
 }
diff --git a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.11.matrix.txt b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.11.matrix.txt
index 646ba9b6a19..646e868d75c 100644
--- a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.11.matrix.txt
+++ b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.11.matrix.txt
@@ -4829,8 +4829,8 @@ C,R,F,B,Bi,Q,ti
 321,12,1,G,234,40,0,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-322,0,0,.,.,.,.,. 0.9880
-322,1,0,.,.,.,.,. 0.0010
+322,0,0,.,.,.,.,. 0.8890
+322,1,0,.,.,.,.,. 0.1000
 322,2,0,.,.,.,.,. 0.0010
 322,3,0,.,.,.,.,. 0.0010
 322,4,0,.,.,.,.,. 0.0010
@@ -4844,8 +4844,8 @@ C,R,F,B,Bi,Q,ti
 322,12,0,.,.,.,.,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-323,0,0,.,.,.,.,. 0.9880
-323,1,0,.,.,.,.,. 0.0010
+323,0,0,.,.,.,.,. 0.8890
+323,1,0,.,.,.,.,. 0.1000
 323,2,0,.,.,.,.,. 0.0010
 323,3,0,.,.,.,.,. 0.0010
 323,4,0,.,.,.,.,. 0.0010
diff --git a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.15.matrix.txt b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.15.matrix.txt
index 1cb867ea2c7..5bea3634699 100644
--- a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.15.matrix.txt
+++ b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.15.matrix.txt
@@ -1994,8 +1994,8 @@ C,R,F,B,Bi,Q,ti
 132,12,1,A,88,40,0,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-133,0,0,.,.,.,.,. 0.9880
-133,1,0,.,.,.,.,. 0.0010
+133,0,0,.,.,.,.,. 0.9764
+133,1,0,.,.,.,.,. 0.0126
 133,2,0,.,.,.,.,. 0.0010
 133,3,0,.,.,.,.,. 0.0010
 133,4,0,.,.,.,.,. 0.0010
@@ -4889,7 +4889,7 @@ C,R,F,B,Bi,Q,ti
 325,12,1,T,227,40,0,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-326,0,0,.,.,.,.,. 0.9880
+326,0,0,.,.,.,.,. 0.9877
 326,1,0,.,.,.,.,. 0.0010
 326,2,0,.,.,.,.,. 0.0010
 326,3,0,.,.,.,.,. 0.0010
@@ -4904,7 +4904,7 @@ C,R,F,B,Bi,Q,ti
 326,12,0,.,.,.,.,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-327,0,0,.,.,.,.,. 0.9880
+327,0,0,.,.,.,.,. 0.9877
 327,1,0,.,.,.,.,. 0.0010
 327,2,0,.,.,.,.,. 0.0010
 327,3,0,.,.,.,.,. 0.0010
@@ -4964,8 +4964,8 @@ C,R,F,B,Bi,Q,ti
 330,12,1,G,229,40,0,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-331,0,0,.,.,.,.,. 0.9880
-331,1,0,.,.,.,.,. 0.0010
+331,0,0,.,.,.,.,. 0.9827
+331,1,0,.,.,.,.,. 0.0063
 331,2,0,.,.,.,.,. 0.0010
 331,3,0,.,.,.,.,. 0.0010
 331,4,0,.,.,.,.,. 0.0010
@@ -4979,8 +4979,8 @@ C,R,F,B,Bi,Q,ti
 331,12,0,.,.,.,.,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-332,0,0,.,.,.,.,. 0.9880
-332,1,0,.,.,.,.,. 0.0010
+332,0,0,.,.,.,.,. 0.9827
+332,1,0,.,.,.,.,. 0.0063
 332,2,0,.,.,.,.,. 0.0010
 332,3,0,.,.,.,.,. 0.0010
 332,4,0,.,.,.,.,. 0.0010
@@ -5009,8 +5009,8 @@ C,R,F,B,Bi,Q,ti
 333,12,3,T,230,20,0,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-334,0,0,.,.,.,.,. 0.9880
-334,1,0,.,.,.,.,. 0.0010
+334,0,0,.,.,.,.,. 0.9827
+334,1,0,.,.,.,.,. 0.0063
 334,2,0,.,.,.,.,. 0.0010
 334,3,0,.,.,.,.,. 0.0010
 334,4,0,.,.,.,.,. 0.0010
diff --git a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.17.matrix.txt b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.17.matrix.txt
index 7fc4955eaa8..c8af93f8912 100644
--- a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.17.matrix.txt
+++ b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.17.matrix.txt
@@ -164,8 +164,8 @@ C,R,F,B,Bi,Q,ti
 10,12,2,A,5,40,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-11,0,0,.,.,.,.,r 0.9880
-11,1,0,.,.,.,.,r 0.0010
+11,0,0,.,.,.,.,r 0.9732
+11,1,0,.,.,.,.,r 0.0158
 11,2,0,.,.,.,.,r 0.0010
 11,3,0,.,.,.,.,r 0.0010
 11,4,0,.,.,.,.,r 0.0010
@@ -179,8 +179,8 @@ C,R,F,B,Bi,Q,ti
 11,12,0,.,.,.,.,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-12,0,0,.,.,.,.,r 0.9880
-12,1,0,.,.,.,.,r 0.0010
+12,0,0,.,.,.,.,r 0.9732
+12,1,0,.,.,.,.,r 0.0158
 12,2,0,.,.,.,.,r 0.0010
 12,3,0,.,.,.,.,r 0.0010
 12,4,0,.,.,.,.,r 0.0010
@@ -209,8 +209,8 @@ C,R,F,B,Bi,Q,ti
 13,12,2,C,7,5,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-14,0,0,.,.,.,.,r 0.9880
-14,1,0,.,.,.,.,r 0.0010
+14,0,0,.,.,.,.,r 0.9096
+14,1,0,.,.,.,.,r 0.0794
 14,2,0,.,.,.,.,r 0.0010
 14,3,0,.,.,.,.,r 0.0010
 14,4,0,.,.,.,.,r 0.0010
@@ -359,8 +359,8 @@ C,R,F,B,Bi,Q,ti
 23,12,1,T,16,16,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-24,0,0,.,.,.,.,r 0.9880
-24,1,0,.,.,.,.,r 0.0010
+24,0,0,.,.,.,.,r 0.9492
+24,1,0,.,.,.,.,r 0.0398
 24,2,0,.,.,.,.,r 0.0010
 24,3,0,.,.,.,.,r 0.0010
 24,4,0,.,.,.,.,r 0.0010
@@ -374,8 +374,8 @@ C,R,F,B,Bi,Q,ti
 24,12,0,.,.,.,.,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-25,0,0,.,.,.,.,r 0.9880
-25,1,0,.,.,.,.,r 0.0010
+25,0,0,.,.,.,.,r 0.9492
+25,1,0,.,.,.,.,r 0.0398
 25,2,0,.,.,.,.,r 0.0010
 25,3,0,.,.,.,.,r 0.0010
 25,4,0,.,.,.,.,r 0.0010
@@ -539,7 +539,7 @@ C,R,F,B,Bi,Q,ti
 35,12,1,T,25,25,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-36,0,0,.,.,.,.,r 0.9880
+36,0,0,.,.,.,.,r 0.9877
 36,1,0,.,.,.,.,r 0.0010
 36,2,0,.,.,.,.,r 0.0010
 36,3,0,.,.,.,.,r 0.0010
@@ -554,7 +554,7 @@ C,R,F,B,Bi,Q,ti
 36,12,0,.,.,.,.,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-37,0,0,.,.,.,.,r 0.9880
+37,0,0,.,.,.,.,r 0.9877
 37,1,0,.,.,.,.,r 0.0010
 37,2,0,.,.,.,.,r 0.0010
 37,3,0,.,.,.,.,r 0.0010
@@ -614,7 +614,7 @@ C,R,F,B,Bi,Q,ti
 40,12,1,G,28,27,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-41,0,0,.,.,.,.,r 0.9880
+41,0,0,.,.,.,.,r 0.9877
 41,1,0,.,.,.,.,r 0.0010
 41,2,0,.,.,.,.,r 0.0010
 41,3,0,.,.,.,.,r 0.0010
@@ -629,7 +629,7 @@ C,R,F,B,Bi,Q,ti
 41,12,0,.,.,.,.,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-42,0,0,.,.,.,.,r 0.9880
+42,0,0,.,.,.,.,r 0.9877
 42,1,0,.,.,.,.,r 0.0010
 42,2,0,.,.,.,.,r 0.0010
 42,3,0,.,.,.,.,r 0.0010
@@ -659,7 +659,7 @@ C,R,F,B,Bi,Q,ti
 43,12,3,T,29,10,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-44,0,0,.,.,.,.,r 0.9880
+44,0,0,.,.,.,.,r 0.9870
 44,1,0,.,.,.,.,r 0.0010
 44,2,0,.,.,.,.,r 0.0010
 44,3,0,.,.,.,.,r 0.0010
@@ -674,7 +674,7 @@ C,R,F,B,Bi,Q,ti
 44,12,0,.,.,.,.,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-45,0,0,.,.,.,.,r 0.9880
+45,0,0,.,.,.,.,r 0.9870
 45,1,0,.,.,.,.,r 0.0010
 45,2,0,.,.,.,.,r 0.0010
 45,3,0,.,.,.,.,r 0.0010
@@ -1694,7 +1694,7 @@ C,R,F,B,Bi,Q,ti
 112,12,1,G,80,28,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-113,0,0,.,.,.,.,r 0.9880
+113,0,0,.,.,.,.,r 0.9874
 113,1,0,.,.,.,.,r 0.0010
 113,2,0,.,.,.,.,r 0.0010
 113,3,0,.,.,.,.,r 0.0010
@@ -1709,7 +1709,7 @@ C,R,F,B,Bi,Q,ti
 113,12,0,.,.,.,.,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-114,0,0,.,.,.,.,r 0.9880
+114,0,0,.,.,.,.,r 0.9874
 114,1,0,.,.,.,.,r 0.0010
 114,2,0,.,.,.,.,r 0.0010
 114,3,0,.,.,.,.,r 0.0010
@@ -2279,8 +2279,8 @@ C,R,F,B,Bi,Q,ti
 151,12,3,T,104,40,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-152,0,0,.,.,.,.,r 0.9880
-152,1,0,.,.,.,.,r 0.0010
+152,0,0,.,.,.,.,r 0.9389
+152,1,0,.,.,.,.,r 0.0501
 152,2,0,.,.,.,.,r 0.0010
 152,3,0,.,.,.,.,r 0.0010
 152,4,0,.,.,.,.,r 0.0010
@@ -2294,8 +2294,8 @@ C,R,F,B,Bi,Q,ti
 152,12,0,.,.,.,.,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-153,0,0,.,.,.,.,r 0.9880
-153,1,0,.,.,.,.,r 0.0010
+153,0,0,.,.,.,.,r 0.9389
+153,1,0,.,.,.,.,r 0.0501
 153,2,0,.,.,.,.,r 0.0010
 153,3,0,.,.,.,.,r 0.0010
 153,4,0,.,.,.,.,r 0.0010
@@ -3074,7 +3074,7 @@ C,R,F,B,Bi,Q,ti
 204,12,1,G,146,21,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-205,0,0,.,.,.,.,r 0.9880
+205,0,0,.,.,.,.,r 0.9877
 205,1,0,.,.,.,.,r 0.0010
 205,2,0,.,.,.,.,r 0.0010
 205,3,0,.,.,.,.,r 0.0010
diff --git a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.23.matrix.txt b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.23.matrix.txt
index 39b384e1b6a..ebcc8b87f50 100644
--- a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.23.matrix.txt
+++ b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.23.matrix.txt
@@ -4484,7 +4484,7 @@ C,R,F,B,Bi,Q,ti
 298,12,1,T,209,40,0,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-299,0,0,.,.,.,.,. 0.9880
+299,0,0,.,.,.,.,. 0.9877
 299,1,0,.,.,.,.,. 0.0010
 299,2,0,.,.,.,.,. 0.0010
 299,3,0,.,.,.,.,. 0.0010
@@ -4499,7 +4499,7 @@ C,R,F,B,Bi,Q,ti
 299,12,0,.,.,.,.,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-300,0,0,.,.,.,.,. 0.9880
+300,0,0,.,.,.,.,. 0.9877
 300,1,0,.,.,.,.,. 0.0010
 300,2,0,.,.,.,.,. 0.0010
 300,3,0,.,.,.,.,. 0.0010
diff --git a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.3.matrix.txt b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.3.matrix.txt
index f34c075b981..f6a4df14858 100644
--- a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.3.matrix.txt
+++ b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.3.matrix.txt
@@ -59,8 +59,8 @@ C,R,F,B,Bi,Q,ti
 3,12,1,C,4,22,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-4,0,0,.,.,.,.,r 0.9880
-4,1,0,.,.,.,.,r 0.0010
+4,0,0,.,.,.,.,r 0.9389
+4,1,0,.,.,.,.,r 0.0501
 4,2,0,.,.,.,.,r 0.0010
 4,3,0,.,.,.,.,r 0.0010
 4,4,0,.,.,.,.,r 0.0010
@@ -1709,8 +1709,8 @@ C,R,F,B,Bi,Q,ti
 113,12,3,T,91,40,0,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-114,0,0,.,.,.,.,r 0.9880
-114,1,0,.,.,.,.,r 0.0010
+114,0,0,.,.,.,.,r 0.9790
+114,1,0,.,.,.,.,r 0.0100
 114,2,0,.,.,.,.,r 0.0010
 114,3,0,.,.,.,.,r 0.0010
 114,4,0,.,.,.,.,r 0.0010
@@ -1724,8 +1724,8 @@ C,R,F,B,Bi,Q,ti
 114,12,0,.,.,.,.,r 0.0010
 
 C,R,F,B,Bi,Q,ti
-115,0,0,.,.,.,.,r 0.9880
-115,1,0,.,.,.,.,r 0.0010
+115,0,0,.,.,.,.,r 0.9790
+115,1,0,.,.,.,.,r 0.0100
 115,2,0,.,.,.,.,r 0.0010
 115,3,0,.,.,.,.,r 0.0010
 115,4,0,.,.,.,.,r 0.0010
diff --git a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.5.matrix.txt b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.5.matrix.txt
index e89186c3366..df837347ab0 100644
--- a/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.5.matrix.txt
+++ b/src/test/resources/org/broadinstitute/hellbender/utils/read/flow/reads/outputs/sample.t0.5.matrix.txt
@@ -5564,8 +5564,8 @@ C,R,F,B,Bi,Q,ti
 370,12,1,G,281,40,0,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-371,0,0,.,.,.,.,. 0.9880
-371,1,0,.,.,.,.,. 0.0010
+371,0,0,.,.,.,.,. 0.9764
+371,1,0,.,.,.,.,. 0.0126
 371,2,0,.,.,.,.,. 0.0010
 371,3,0,.,.,.,.,. 0.0010
 371,4,0,.,.,.,.,. 0.0010
@@ -5579,8 +5579,8 @@ C,R,F,B,Bi,Q,ti
 371,12,0,.,.,.,.,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-372,0,0,.,.,.,.,. 0.9880
-372,1,0,.,.,.,.,. 0.0010
+372,0,0,.,.,.,.,. 0.9764
+372,1,0,.,.,.,.,. 0.0126
 372,2,0,.,.,.,.,. 0.0010
 372,3,0,.,.,.,.,. 0.0010
 372,4,0,.,.,.,.,. 0.0010
@@ -5609,8 +5609,8 @@ C,R,F,B,Bi,Q,ti
 373,12,2,T,282,14,0,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-374,0,0,.,.,.,.,. 0.9880
-374,1,0,.,.,.,.,. 0.0010
+374,0,0,.,.,.,.,. 0.9840
+374,1,0,.,.,.,.,. 0.0050
 374,2,0,.,.,.,.,. 0.0010
 374,3,0,.,.,.,.,. 0.0010
 374,4,0,.,.,.,.,. 0.0010
@@ -5624,8 +5624,8 @@ C,R,F,B,Bi,Q,ti
 374,12,0,.,.,.,.,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-375,0,0,.,.,.,.,. 0.9880
-375,1,0,.,.,.,.,. 0.0010
+375,0,0,.,.,.,.,. 0.9840
+375,1,0,.,.,.,.,. 0.0050
 375,2,0,.,.,.,.,. 0.0010
 375,3,0,.,.,.,.,. 0.0010
 375,4,0,.,.,.,.,. 0.0010
@@ -5684,8 +5684,8 @@ C,R,F,B,Bi,Q,ti
 378,12,1,G,285,26,0,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-379,0,0,.,.,.,.,. 0.9880
-379,1,0,.,.,.,.,. 0.0010
+379,0,0,.,.,.,.,. 0.9850
+379,1,0,.,.,.,.,. 0.0040
 379,2,0,.,.,.,.,. 0.0010
 379,3,0,.,.,.,.,. 0.0010
 379,4,0,.,.,.,.,. 0.0010
@@ -5699,8 +5699,8 @@ C,R,F,B,Bi,Q,ti
 379,12,0,.,.,.,.,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-380,0,0,.,.,.,.,. 0.9880
-380,1,0,.,.,.,.,. 0.0010
+380,0,0,.,.,.,.,. 0.9850
+380,1,0,.,.,.,.,. 0.0040
 380,2,0,.,.,.,.,. 0.0010
 380,3,0,.,.,.,.,. 0.0010
 380,4,0,.,.,.,.,. 0.0010
@@ -5864,7 +5864,7 @@ C,R,F,B,Bi,Q,ti
 390,12,1,G,293,22,0,. 0.0010
 
 C,R,F,B,Bi,Q,ti
-391,0,0,.,.,.,.,. 0.9880
+391,0,0,.,.,.,.,. 0.9874
 391,1,0,.,.,.,.,. 0.0010
 391,2,0,.,.,.,.,. 0.0010
 391,3,0,.,.,.,.,. 0.0010

From 39cf1fc05175044e50e723f66302ad69a99bdfad Mon Sep 17 00:00:00 2001
From: Ilya Soifer <ilya.soifer@ultimagen.com>
Date: Tue, 21 Feb 2023 09:58:47 +0200
Subject: [PATCH 3/3] PR comment

---
 .../hellbender/utils/read/FlowBasedRead.java               | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java b/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java
index 706e48d0d6b..f5030a3f655 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java
@@ -358,7 +358,12 @@ private void parseSingleHmer(final double[] probs, final byte[] tp, final int fl
         }
     }
 
-    //convert qualities from the single hmer to a column in a flow matrix
+    // convert qualities from the t0 tag to the probabilities of 1->0 error.
+    // This function deals with t0 tag that encodes the probability of 1->0 error
+    // in this case there is no nucleotide to place the error probability on, so we
+    // place it on the neighboring bases and choose the **lower** error probability between the
+    // neighbors (that's how T0 encoding works). The error is placed only on the 1-mer error assuming
+    // that 2->0 errors are negligibly rare.
     private void parseZeroQuals(final double[] probs, final int flowIdx, final int qualOfs){
         if ((qualOfs == 0) | (qualOfs==probs.length)){ // do not report zero error probability on the edge of the read
             return;