disabled test illustrating a very gross problem

broadinstitute · Jul 12, 2019 · 8979ee9 · 8979ee9
1 parent 6f4d486
commit 8979ee9
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/...bender/tools/walkers/haplotypecaller/graphs/JunctionTreeKBestHaplotypeFinderUnitTest.java b/...bender/tools/walkers/haplotypecaller/graphs/JunctionTreeKBestHaplotypeFinderUnitTest.java
@@ -31,12 +31,12 @@ public static byte[] getBytes(final String alignment) {
     @DataProvider (name = "loopingReferences")
     public static Object[][] loopingReferencesRecoverablehaplotypes() {
         return new Object[][]{
-//                new Object[]{"GACACACAGTCA", 3, 8, true}, //ACA and CAC are repeated, 9 is enough bases to span the path
-//                new Object[]{"GACACACAGTCA", 3, 5, false}, //ACA and CAC are repeated, 8 is not
-//                new Object[]{"GACACTCACGCACGG", 3, 6, true}, //CAC repeated thrice, showing that the loops are handled somewhat sanely
-//                new Object[]{"GACATCGACGG", 3, 11, false}, //GAC repeated twice, starting with GAC, can it recover the reference if it starts on a repeated kmer
-//                new Object[]{"GACATCGACGG", 3, 6, false}, //With non-unique reference start we fall over for looping structures todo
-//                new Object[]{"GACATCGACGG", 3, 6, false}, //reads too short to be resolvable
+                new Object[]{"GACACACAGTCA", 3, 8, true}, //ACA and CAC are repeated, 9 is enough bases to span the path
+                new Object[]{"GACACACAGTCA", 3, 5, false}, //ACA and CAC are repeated, 8 is not
+                new Object[]{"GACACTCACGCACGG", 3, 6, true}, //CAC repeated thrice, showing that the loops are handled somewhat sanely
+                new Object[]{"GACATCGACGG", 3, 11, false}, //GAC repeated twice, starting with GAC, can it recover the reference if it starts on a repeated kmer
+                new Object[]{"GACATCGACGG", 3, 6, false}, //With non-unique reference start we fall over for looping structures todo
+                new Object[]{"GACATCGACGG", 3, 6, false}, //reads too short to be resolvable
                 new Object[]{"GACATCACATC", 3, 8, true}, //final kmer ATC is repeated, can we recover the reference for repating final kmer
 
                 // Some less complicated cases
@@ -72,7 +72,7 @@ public void testRecoveryOfLoopingReferenceSequences(final String ref, final int
         }
     }
 
-    @Test (dataProvider = "loopingReferences")
+    @Test (enabled = false)
     //TODO this case fails because without reference weight we might end up looping forever in some gross structure and never stopping....
     //TODO either restrict paths based onthe reference or do something smarter to prevent infinite loops....
     public void testDegenerateLoopingCase() {