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[ADAM-1141] Add support for saving/loading AlignmentRecords to/from C…
…RAM. Resolves bigdatagenomics#1141. Changes the signature of `AlignmentRecordRDD.saveAsSAM` to take an `Option[SAMFormat]` parameter, since `asSam` is now no longer a binary choice.
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMCRAMOutputFormat.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.rdd.read | ||
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| import htsjdk.samtools.SAMFileHeader | ||
| import org.apache.hadoop.fs.Path | ||
| import org.apache.hadoop.mapreduce.{ OutputFormat, RecordWriter, TaskAttemptContext } | ||
| import org.apache.spark.rdd.InstrumentedOutputFormat | ||
| import org.bdgenomics.adam.instrumentation.Timers | ||
| import org.seqdoop.hadoop_bam.{ | ||
| KeyIgnoringCRAMOutputFormat, | ||
| KeyIgnoringCRAMRecordWriter, | ||
| SAMRecordWritable | ||
| } | ||
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| class ADAMCRAMOutputFormat[K] | ||
| extends KeyIgnoringCRAMOutputFormat[K] with Serializable { | ||
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| setWriteHeader(true) | ||
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| override def getRecordWriter(context: TaskAttemptContext): RecordWriter[K, SAMRecordWritable] = { | ||
| val conf = context.getConfiguration() | ||
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| // where is our header file? | ||
| val path = new Path(conf.get("org.bdgenomics.adam.rdd.read.bam_header_path")) | ||
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| // read the header file | ||
| readSAMHeaderFrom(path, conf) | ||
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| // now that we have the header set, we need to make a record reader | ||
| return new KeyIgnoringCRAMRecordWriter[K](getDefaultWorkFile(context, ""), | ||
| header, | ||
| true, | ||
| context) | ||
| } | ||
| } | ||
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| class InstrumentedADAMCRAMOutputFormat[K] extends InstrumentedOutputFormat[K, org.seqdoop.hadoop_bam.SAMRecordWritable] { | ||
| override def timerName(): String = Timers.WriteCRAMRecord.timerName | ||
| override def outputFormatClass(): Class[_ <: OutputFormat[K, SAMRecordWritable]] = classOf[ADAMCRAMOutputFormat[K]] | ||
| } | ||
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| class ADAMCRAMOutputFormatHeaderLess[K] | ||
| extends KeyIgnoringCRAMOutputFormat[K] with Serializable { | ||
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| setWriteHeader(false) | ||
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| override def getRecordWriter(context: TaskAttemptContext): RecordWriter[K, SAMRecordWritable] = { | ||
| val conf = context.getConfiguration() | ||
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| // where is our header file? | ||
| val path = new Path(conf.get("org.bdgenomics.adam.rdd.read.bam_header_path")) | ||
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| // read the header file | ||
| readSAMHeaderFrom(path, conf) | ||
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| // now that we have the header set, we need to make a record reader | ||
| return new KeyIgnoringCRAMRecordWriter[K](getDefaultWorkFile(context, ""), | ||
| header, | ||
| false, | ||
| context) | ||
| } | ||
| } | ||
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| class InstrumentedADAMCRAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, org.seqdoop.hadoop_bam.SAMRecordWritable] { | ||
| override def timerName(): String = Timers.WriteCRAMRecord.timerName | ||
| override def outputFormatClass(): Class[_ <: OutputFormat[K, SAMRecordWritable]] = classOf[ADAMCRAMOutputFormatHeaderLess[K]] | ||
| } |
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