Update to AlignmentRecordField and its usages as contig changed to co…

…ntigName in alignmentRecord
heuermh · Apr 7, 2016 · 500c1cb · 500c1cb
1 parent 47dfa4d
commit 500c1cb
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Showing 6 changed files with 10 additions and 10 deletions.
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CalculateDepth.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CalculateDepth.scala
@@ -65,7 +65,7 @@ class CalculateDepth(protected val args: CalculateDepthArgs) extends BDGSparkCom
 
   def run(sc: SparkContext): Unit = {
 
-    val proj = Projection(contig, start, cigar, readMapped)
+    val proj = Projection(contigName, start, cigar, readMapped)
 
     val adamRDD: RDD[AlignmentRecord] = sc.loadAlignments(args.adamInputPath, projection = Some(proj))
     val mappedRDD = adamRDD.filter(_.getReadMapped)

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/FlagStat.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/FlagStat.scala
@@ -54,8 +54,8 @@ class FlagStat(protected val args: FlagStatArgs) extends BDGSparkCommand[FlagSta
       AlignmentRecordField.readMapped,
       AlignmentRecordField.mateMapped,
       AlignmentRecordField.readPaired,
-      AlignmentRecordField.contig,
-      AlignmentRecordField.mateContig,
+      AlignmentRecordField.contigName,
+      AlignmentRecordField.mateContigName,
       AlignmentRecordField.primaryAlignment,
       AlignmentRecordField.duplicateRead,
       AlignmentRecordField.readMapped,

diff --git a/adam-cli/src/test/scala/org/bdgenomics/adam/cli/FlagStatSuite.scala b/adam-cli/src/test/scala/org/bdgenomics/adam/cli/FlagStatSuite.scala
@@ -39,8 +39,8 @@ class FlagStatSuite extends ADAMFunSuite {
       AlignmentRecordField.readMapped,
       AlignmentRecordField.mateMapped,
       AlignmentRecordField.readPaired,
-      AlignmentRecordField.contig,
-      AlignmentRecordField.mateContig,
+      AlignmentRecordField.contigName,
+      AlignmentRecordField.mateContigName,
       AlignmentRecordField.primaryAlignment,
       AlignmentRecordField.duplicateRead,
       AlignmentRecordField.readMapped,

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/projections/AlignmentRecordField.scala b/adam-core/src/main/scala/org/bdgenomics/adam/projections/AlignmentRecordField.scala
@@ -28,5 +28,5 @@ import org.bdgenomics.formats.avro.AlignmentRecord
  */
 object AlignmentRecordField extends FieldEnumeration(AlignmentRecord.SCHEMA$) {
 
-  val contig, start, end, mapq, readName, sequence, mateAlignmentStart, cigar, qual, recordGroupId, recordGroupName, readPaired, properPair, readMapped, mateMapped, readNegativeStrand, mateNegativeStrand, readInFragment, primaryAlignment, failedVendorQualityChecks, duplicateRead, mismatchingPositions, attributes, recordGroupSequencingCenter, recordGroupDescription, recordGroupRunDateEpoch, recordGroupFlowOrder, recordGroupKeySequence, recordGroupLibrary, recordGroupPredictedMedianInsertSize, recordGroupPlatform, recordGroupPlatformUnit, recordGroupSample, mateContig, origQual, supplementaryAlignment, secondaryAlignment = SchemaValue
+  val contigName, start, end, mapq, readName, sequence, mateAlignmentStart, cigar, qual, recordGroupId, recordGroupName, readPaired, properPair, readMapped, mateMapped, readNegativeStrand, mateNegativeStrand, readInFragment, primaryAlignment, failedVendorQualityChecks, duplicateRead, mismatchingPositions, attributes, recordGroupSequencingCenter, recordGroupDescription, recordGroupRunDateEpoch, recordGroupFlowOrder, recordGroupKeySequence, recordGroupLibrary, recordGroupPredictedMedianInsertSize, recordGroupPlatform, recordGroupPlatformUnit, recordGroupSample, mateContigName, origQual, supplementaryAlignment, secondaryAlignment = SchemaValue
 }
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
@@ -206,8 +206,8 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     val projection =
       if (isADAMRecord) {
         Projection(
-          AlignmentRecordField.contig,
-          AlignmentRecordField.mateContig,
+          AlignmentRecordField.contigName,
+          AlignmentRecordField.mateContigName,
           AlignmentRecordField.readPaired,
           AlignmentRecordField.readInFragment,
           AlignmentRecordField.readMapped,
@@ -216,7 +216,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
       } else if (isADAMContig) {
         Projection(NucleotideContigFragmentField.contig)
       } else {
-        Projection(AlignmentRecordField.contig)
+        Projection(AlignmentRecordField.contigName)
       }
 
     if (filePath.endsWith(".bam") || filePath.endsWith(".sam")) {

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicPositionPartitionerSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicPositionPartitionerSuite.scala
@@ -102,7 +102,7 @@ class GenomicPositionPartitionerSuite extends ADAMFunSuite {
 
     val p = {
       import org.bdgenomics.adam.projections.AlignmentRecordField._
-      Projection(contig, start, readName, readMapped)
+      Projection(contigName, start, readName, readMapped)
     }
     val rdd: RDD[AlignmentRecord] = sc.loadAlignments(filename, projection = Some(p))