From 74b08a03ffbad5e7aca757c4200cbd87728f8682 Mon Sep 17 00:00:00 2001
From: Mark Walker <markw@broadinstitute.org>
Date: Fri, 3 Apr 2020 12:52:51 -0400
Subject: [PATCH] Delete unused validate function

---
 .../hellbender/tools/spark/pathseq/PSFilter.java         | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PSFilter.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PSFilter.java
index 74eb3871f82..f6631ca2849 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PSFilter.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PSFilter.java
@@ -216,15 +216,6 @@ static JavaRDD<GATKRead> doBwaFilter(final JavaRDD<GATKRead> reads,
         return reads.mapPartitions(itr -> (new PSBwaFilter(indexFileName, minIdentity, minSeedLength, numThreads, false)).apply(itr));
     }
 
-    private static void validateIgnoredContigs(final List<String> contigs, final SAMSequenceDictionary dictionary) {
-        final Set<String> contigsToIgnoreSet = new HashSet<>();
-        for (final String contig : contigsToIgnoreSet) {
-            if (dictionary.getSequence(contig) == null) {
-                throw new UserException.MissingContigInSequenceDictionary(contig, dictionary);
-            }
-        }
-    }
-
     /**
      * Main PathSeq filtering method. See PathSeqFilterSpark for an overview.
      * Returns a tuple containing the paired reads and unpaired reads as separate RDDs.