From e41747a5e655c4d87cceb863bffb602c9cc68540 Mon Sep 17 00:00:00 2001
From: Ilya Soifer <ilya.soifer@ultimagen.com>
Date: Mon, 13 Nov 2023 20:05:38 +0200
Subject: [PATCH] Removes unnecessary and buggy validation check (#8580)

* Additional fix + logging fixes
* Added missing initialization
---
 .../haplotypecaller/AlleleFiltering.java        |  2 +-
 .../hellbender/utils/read/FlowBasedRead.java    | 17 +++--------------
 .../utils/read/FlowBasedReadUtils.java          |  2 +-
 3 files changed, 5 insertions(+), 16 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFiltering.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFiltering.java
index 17728fa6035..ebc0f61d3f6 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFiltering.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFiltering.java
@@ -340,7 +340,7 @@ private AlleleLikelihoods<GATKRead, Allele> getAlleleLikelihoodMatrix(final Alle
                 .forEach(alleleHaplotypeMap.get(notAllele)::add);
 
         final AlleleLikelihoods<GATKRead, Allele> alleleLikelihoods = readLikelihoods.marginalize(alleleHaplotypeMap);
-        logger.debug(() -> String.format("GALM: %s %d %d", allele.toString(), alleleHaplotypeMap.get(allele).size(), alleleHaplotypeMap.get(notAllele).size()));
+        logger.debug(() -> String.format("GALM: %s %d %d", allele, alleleHaplotypeMap.get(allele.altAllele()).size(), alleleHaplotypeMap.get(notAllele).size()));
         return alleleLikelihoods;
     }
 
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 75a30c2a8d3..273761b0318 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java
@@ -41,7 +41,7 @@ public class FlowBasedRead extends SAMRecordToGATKReadAdapter implements GATKRea
     public static final int  MAX_CLASS = 12; //note - this is a historical value to support files with max class is not defined in the header, it is expected that mc tag exists in the CRAM
     public static final String     DEFAULT_FLOW_ORDER = "TGCA";
     private static final long serialVersionUID = 42L;
-    private final Logger logger = LogManager.getLogger(this.getClass());
+    private static final Logger logger = LogManager.getLogger(FlowBasedRead.class);
     private static final OneShotLogger vestigialOneShotLogger = new OneShotLogger(FlowBasedRead.class);
 
     // constants
@@ -117,7 +117,7 @@ public class FlowBasedRead extends SAMRecordToGATKReadAdapter implements GATKRea
      * The validity status of the key. Certain operations may produce undefined/errornous results. This is signaled by
      * the read being marked with a validKey == false
      */
-    private boolean validKey;
+    private boolean validKey = true;
 
     /**
      * The direction of this read. After being red, the direction will also swing to be REFERENCE
@@ -248,7 +248,6 @@ public FlowBasedRead(final SAMRecord samRecord, final String flowOrder, final in
             logger.debug("       key: " + FlowBasedKeyCodec.keyAsString(key));
         }
 
-        validateSequence();
     }
 
     //since the last unclipped flow is uncertain (we give high probabilities to
@@ -428,16 +427,6 @@ private int[] getAttributeAsIntArray(final String attributeName, final boolean i
         }
     }
 
-
-    private void validateSequence(){
-        for (final int b : key) {
-            if (b > maxHmer - 1) {
-                validKey = false;
-            }
-        }
-        validKey = true;
-    }
-
     public boolean isValid() {
         return validKey;
     }
@@ -584,6 +573,7 @@ public void applyBaseClipping(final int clipLeftBase, final int clipRightBase, b
         } else {
             applyClipping(clipLeft, leftHmerClip, clipRight, rightHmerClip, spread);
             baseClipped = true;
+            validKey = true;
             trimLeftBase = clipLeftBase;
             trimRightBase = clipRightBase;
         }
@@ -1109,7 +1099,6 @@ private void readVestigialFlowMatrixFromKR(final String _flowOrder) {
         final double [] kdProbs = phredToProb(kd);
         fillFlowMatrix( kh, kf, kdProbs);
         applyFilteringFlowMatrix();
-        validateSequence();
     }
 
 }
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 d7a7a76faaf..ff009611521 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtils.java
@@ -303,7 +303,7 @@ public static int getMarkDupReadStart(final GATKRead gatkRead, final boolean end
                     hmersLeft--;
                 }
 
-            int         hmerSize = 1;
+            int hmerSize = 1;
             for ( ; hmerSize < bases.length ; hmerSize++ )
                 if (bases[hmerSize] != hmerBase) {
                     if ( --hmersLeft <= 0 )