[ADAM-1488] Only increment BQSR min quality by 33 once.

Resolves bigdatagenomics#1488.
fnothaft · Apr 14, 2017 · 04444aa · 04444aa
1 parent 6c32a02
commit 04444aa
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
@@ -645,7 +645,7 @@ case class AlignmentRecordRDD(
     replaceRdd(BaseQualityRecalibration(rdd,
       knownSnps,
       recordGroups,
-      (minAcceptableQuality + 33).toChar,
+      minAcceptableQuality,
       optStorageLevel))
   }
 

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/RecalibrationTable.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/RecalibrationTable.scala
@@ -49,7 +49,7 @@ private[adam] case class RecalibrationTable private[recalibration] (
       var idx = 0
       while (idx < numCovariates) {
         val key = covariates(idx)
-        newQuals(idx) = table.getOrElse(key, key.quality)
+        newQuals(idx) = table.getOrElse(key.toDefault, key.quality)
         idx += 1
       }
     }
@@ -200,7 +200,7 @@ private[recalibration] object RecalibrationTable {
     val recalibrationQualityMappings = InvertingRecalibrationTable.time {
       observed.entries
         .keys
-        .map(key => (key, tt.lookup(key)))
+        .map(key => (key.toDefault, tt.lookup(key)))
         .toMap
     }
 

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Recalibrator.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Recalibrator.scala
@@ -66,7 +66,7 @@ private[recalibration] case class Recalibrator(
                           covariates: Array[CovariateKey]): String = ComputeQualityScore.time {
     val origQuals = read.getQual
     val quals = new StringBuilder(origQuals)
-    val newQuals = table(covariates.map(_.toDefault))
+    val newQuals = table(covariates)
     var idx = 0
     while (idx < origQuals.length) {
       // Keep original quality score if below recalibration threshold