forked from bigdatagenomics/adam
/
SAMFileHeaderWritable.scala
79 lines (71 loc) · 2.73 KB
/
SAMFileHeaderWritable.scala
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/**
* Licensed to Big Data Genomics (BDG) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The BDG licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.bdgenomics.adam.models
import htsjdk.samtools.SAMFileHeader
import org.bdgenomics.adam.rdd.ADAMContext
import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD
import scala.collection.JavaConversions._
private[adam] object SAMFileHeaderWritable {
/**
* Creates a serializable representation of a SAM file header.
*
* @param header SAMFileHeader to create serializable representation of.
* @return A serializable representation of the header that can be transformed
* back into the htsjdk representation on the executor.
*/
def apply(header: SAMFileHeader): SAMFileHeaderWritable = {
new SAMFileHeaderWritable(header)
}
}
/**
* Wrapper for the SAM file header to get around serialization issues.
*
* The SAM file header is not serialized and is instead recreated on demaind.
*
* @param hdr A SAM file header to extract metadata from.
*/
private[adam] class SAMFileHeaderWritable private (hdr: SAMFileHeader) extends Serializable {
// extract fields that are needed in order to recreate the SAMFileHeader
private val text = {
val txt: String = hdr.getTextHeader
Option(txt)
}
private val sd = SequenceDictionary(hdr.getSequenceDictionary)
private val pgl = {
val pgs = hdr.getProgramRecords
pgs.map(ADAMContext.convertSAMProgramRecord)
}
private val comments = {
val cmts = hdr.getComments
cmts.flatMap(Option(_)) // don't trust samtools to return non-nulls
}
private val rgs = RecordGroupDictionary.fromSAMHeader(hdr)
/**
* Recreate header when requested to get around header not being serializable.
*/
@transient lazy val header = {
val h = new SAMFileHeader()
// add back optional fields
text.foreach(h.setTextHeader)
h.setSequenceDictionary(sd.toSAMSequenceDictionary)
pgl.foreach(p => h.addProgramRecord(AlignmentRecordRDD.processingStepToSam(p)))
comments.foreach(h.addComment)
rgs.recordGroups.foreach(rg => h.addReadGroup(rg.toSAMReadGroupRecord))
h
}
}