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[ADAM-942] Replace first/secondInRead with readInFragment #943

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merged 1 commit into from Feb 15, 2016
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replace first/secondInRead with readInFragment, fixes #942

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heuermh committed Feb 13, 2016
commit 2996ee644307c312fd9e8e75c560627a2c21b300
@@ -62,8 +62,7 @@ class Adam2Fastq(val args: Adam2FastqArgs) extends BDGSparkCommand[Adam2FastqArg
AlignmentRecordField.readName,
AlignmentRecordField.sequence,
AlignmentRecordField.qual,
AlignmentRecordField.firstOfPair,
AlignmentRecordField.secondOfPair,
AlignmentRecordField.readInFragment,
AlignmentRecordField.origQual
)
)
@@ -58,8 +58,7 @@ class FlagStat(protected val args: FlagStatArgs) extends BDGSparkCommand[FlagSta
AlignmentRecordField.duplicateRead,
AlignmentRecordField.readMapped,
AlignmentRecordField.mateMapped,
AlignmentRecordField.firstOfPair,
AlignmentRecordField.secondOfPair,
AlignmentRecordField.readInFragment,
AlignmentRecordField.properPair,
AlignmentRecordField.mapq,
AlignmentRecordField.failedVendorQualityChecks
@@ -45,8 +45,7 @@ class FlagStatSuite extends ADAMFunSuite {
AlignmentRecordField.duplicateRead,
AlignmentRecordField.readMapped,
AlignmentRecordField.mateMapped,
AlignmentRecordField.firstOfPair,
AlignmentRecordField.secondOfPair,
AlignmentRecordField.readInFragment,
AlignmentRecordField.properPair,
AlignmentRecordField.mapq,
AlignmentRecordField.failedVendorQualityChecks)
@@ -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, firstOfPair, secondOfPair, primaryAlignment, failedVendorQualityChecks, duplicateRead, mismatchingPositions, attributes, recordGroupSequencingCenter, recordGroupDescription, recordGroupRunDateEpoch, recordGroupFlowOrder, recordGroupKeySequence, recordGroupLibrary, recordGroupPredictedMedianInsertSize, recordGroupPlatform, recordGroupPlatformUnit, recordGroupSample, mateContig, origQual, supplementaryAlignment, secondaryAlignment = SchemaValue
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
}
@@ -208,7 +208,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
AlignmentRecordField.contig,
AlignmentRecordField.mateContig,
AlignmentRecordField.readPaired,
AlignmentRecordField.firstOfPair,
AlignmentRecordField.readInFragment,
AlignmentRecordField.readMapped,
AlignmentRecordField.mateMapped
)
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