Deprecate SAMFileHeaderWriteable.

bigdatagenomics · Jun 12, 2019 · b58e2c7 · b58e2c7
1 parent 38973ae
commit b58e2c7
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Showing 8 changed files with 30 additions and 30 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
@@ -233,11 +233,11 @@ class AlignmentRecordConverter extends Serializable {
    * @return Returns the record converted to htsjdk format. Can be used for output to SAM/BAM.
    */
   def convert(adamRecord: AlignmentRecord,
-              header: SAMFileHeaderWritable,
+              header: SAMFileHeader,
               rgd: ReadGroupDictionary): SAMRecord = ConvertToSAMRecord.time {
 
     // attach header
-    val builder: SAMRecord = new SAMRecord(header.header)
+    val builder: SAMRecord = new SAMRecord(header)
 
     // set canonically necessary fields
     builder.setReadName(adamRecord.getReadName)

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala
@@ -22,6 +22,9 @@ import org.bdgenomics.adam.rdd.ADAMContext
 import org.bdgenomics.adam.rdd.read.AlignmentRecordDataset
 import scala.collection.JavaConversions._
 
+/**
+ * @deprecated no longer necessary, SAMFileHeader implements Serializable
+ */
 private[adam] object SAMFileHeaderWritable {
 
   /**

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.scala
@@ -725,7 +725,7 @@ sealed abstract class AlignmentRecordDataset extends AvroReadGroupGenomicDataset
     header.setProgramRecords(pgRecords.asJava)
 
     // broadcast for efficiency
-    val hdrBcast = rdd.context.broadcast(SAMFileHeaderWritable(header))
+    val hdrBcast = rdd.context.broadcast(header)
 
     // map across RDD to perform conversion
     val convertedRDD: RDD[SAMRecordWritable] = rdd.map(r => {

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMInFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMInFormatter.scala
@@ -20,10 +20,7 @@ package org.bdgenomics.adam.rdd.read
 import htsjdk.samtools.{ SAMFileHeader, SAMFileWriter }
 import java.io.OutputStream
 import org.bdgenomics.adam.converters.AlignmentRecordConverter
-import org.bdgenomics.adam.models.{
-  ReadGroupDictionary,
-  SAMFileHeaderWritable
-}
+import org.bdgenomics.adam.models.ReadGroupDictionary
 import org.bdgenomics.adam.rdd.{ InFormatter, InFormatterCompanion }
 import org.bdgenomics.adam.sql.{ AlignmentRecord => AlignmentRecordProduct }
 import org.bdgenomics.formats.avro.AlignmentRecord
@@ -35,7 +32,7 @@ import org.bdgenomics.formats.avro.AlignmentRecord
  * @tparam T The type of the underlying InFormatter.
  */
 trait AnySAMInFormatterCompanion[T <: AnySAMInFormatter[T]] extends InFormatterCompanion[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordDataset, T] {
-  protected def makeFormatter(header: SAMFileHeaderWritable,
+  protected def makeFormatter(header: SAMFileHeader,
                               readGroups: ReadGroupDictionary,
                               converter: AlignmentRecordConverter): T
 
@@ -55,7 +52,7 @@ trait AnySAMInFormatterCompanion[T <: AnySAMInFormatter[T]] extends InFormatterC
     header.setSortOrder(SAMFileHeader.SortOrder.coordinate)
 
     // construct the in formatter
-    makeFormatter(SAMFileHeaderWritable(header), gDataset.readGroups, arc)
+    makeFormatter(header, gDataset.readGroups, arc)
   }
 }
 
@@ -69,7 +66,7 @@ trait AnySAMInFormatter[T <: AnySAMInFormatter[T]] extends InFormatter[Alignment
   /**
    * A serializable form of the SAM File Header.
    */
-  val header: SAMFileHeaderWritable
+  val header: SAMFileHeader
 
   /**
    * A dictionary describing the read groups these reads are from.

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/BAMInFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/BAMInFormatter.scala
@@ -18,37 +18,35 @@
 package org.bdgenomics.adam.rdd.read
 
 import htsjdk.samtools.{
+  SAMFileHeader,
   SAMFileWriter,
   SAMFileWriterFactory
 }
 import java.io.OutputStream
 import org.bdgenomics.adam.converters.AlignmentRecordConverter
-import org.bdgenomics.adam.models.{
-  ReadGroupDictionary,
-  SAMFileHeaderWritable
-}
+import org.bdgenomics.adam.models.ReadGroupDictionary
 
 /**
  * InFormatter companion for building an InFormatter that streams BAM.
  */
 object BAMInFormatter extends AnySAMInFormatterCompanion[BAMInFormatter] {
 
-  protected def makeFormatter(header: SAMFileHeaderWritable,
+  protected def makeFormatter(header: SAMFileHeader,
                               readGroups: ReadGroupDictionary,
                               converter: AlignmentRecordConverter): BAMInFormatter = {
     BAMInFormatter(header, readGroups, converter)
   }
 }
 
 case class BAMInFormatter private (
-    header: SAMFileHeaderWritable,
+    header: SAMFileHeader,
     readGroups: ReadGroupDictionary,
     converter: AlignmentRecordConverter) extends AnySAMInFormatter[BAMInFormatter] {
 
   protected val companion = BAMInFormatter
 
   protected def makeWriter(os: OutputStream): SAMFileWriter = {
     new SAMFileWriterFactory()
-      .makeBAMWriter(header.header, true, os)
+      .makeBAMWriter(header, true, os)
   }
 }
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/SAMInFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/SAMInFormatter.scala
@@ -18,30 +18,28 @@
 package org.bdgenomics.adam.rdd.read
 
 import htsjdk.samtools.{
+  SAMFileHeader,
   SAMFileWriter,
   SAMFileWriterFactory
 }
 import java.io.OutputStream
 import org.bdgenomics.adam.converters.AlignmentRecordConverter
-import org.bdgenomics.adam.models.{
-  ReadGroupDictionary,
-  SAMFileHeaderWritable
-}
+import org.bdgenomics.adam.models.ReadGroupDictionary
 
 /**
  * InFormatter companion for building an InFormatter that streams SAM.
  */
 object SAMInFormatter extends AnySAMInFormatterCompanion[SAMInFormatter] {
 
-  protected def makeFormatter(header: SAMFileHeaderWritable,
+  protected def makeFormatter(header: SAMFileHeader,
                               readGroups: ReadGroupDictionary,
                               converter: AlignmentRecordConverter): SAMInFormatter = {
     SAMInFormatter(header, readGroups, converter)
   }
 }
 
 case class SAMInFormatter private (
-    header: SAMFileHeaderWritable,
+    header: SAMFileHeader,
     readGroups: ReadGroupDictionary,
     converter: AlignmentRecordConverter) extends AnySAMInFormatter[SAMInFormatter] {
 
@@ -53,6 +51,6 @@ case class SAMInFormatter private (
 
   protected def makeWriter(os: OutputStream): SAMFileWriter = {
     new SAMFileWriterFactory()
-      .makeSAMWriter(header.header, true, os)
+      .makeSAMWriter(header, true, os)
   }
 }
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala b/adam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala
@@ -111,9 +111,13 @@ class ADAMKryoRegistrator extends KryoRegistrator with Logging {
     kryo.register(classOf[htsjdk.samtools.CigarElement])
     kryo.register(classOf[htsjdk.samtools.CigarOperator])
     kryo.register(classOf[htsjdk.samtools.Cigar])
+    kryo.register(classOf[htsjdk.samtools.SAMProgramRecord])
+    kryo.register(classOf[htsjdk.samtools.SAMReadGroupRecord])
     kryo.register(classOf[htsjdk.samtools.SAMSequenceDictionary])
     kryo.register(classOf[htsjdk.samtools.SAMFileHeader])
     kryo.register(classOf[htsjdk.samtools.SAMSequenceRecord])
+    registerByName(kryo, "htsjdk.samtools.SAMFileHeader$GroupOrder")
+    registerByName(kryo, "htsjdk.samtools.SAMFileHeader$SortOrder")
 
     // htsjdk.variant.vcf
     kryo.register(classOf[htsjdk.variant.vcf.VCFContigHeaderLine])

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala
@@ -17,12 +17,14 @@
  */
 package org.bdgenomics.adam.converters
 
-import htsjdk.samtools.SamReaderFactory
+import htsjdk.samtools.{
+  SAMFileHeader,
+  SamReaderFactory
+}
 import java.io.File
 import org.bdgenomics.adam.models.{
   ReadGroupDictionary,
   ReadGroup,
-  SAMFileHeaderWritable,
   SequenceDictionary,
   SequenceRecord
 }
@@ -79,8 +81,7 @@ class AlignmentRecordConverterSuite extends FunSuite {
 
     // convert read
     val toSAM = adamRecordConverter.convert(adamRead,
-      SAMFileHeaderWritable(adamRecordConverter.createSAMHeader(dict,
-        readGroups)),
+      adamRecordConverter.createSAMHeader(dict, readGroups),
       readGroups)
 
     // validate conversion
@@ -122,8 +123,7 @@ class AlignmentRecordConverterSuite extends FunSuite {
 
     // convert read
     val toSAM = adamRecordConverter.convert(adamRead,
-      SAMFileHeaderWritable(adamRecordConverter.createSAMHeader(dict,
-        readGroups)),
+      adamRecordConverter.createSAMHeader(dict, readGroups),
       readGroups)
 
     // validate conversion