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[ADAM-916] New strategy for writing header. #917

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Jan 14, 2016
Merged

[ADAM-916] New strategy for writing header. #917

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29 changes: 25 additions & 4 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMBAMOutputFormat.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,17 @@
*/
package org.bdgenomics.adam.rdd.read

import org.seqdoop.hadoop_bam.{ SAMRecordWritable, KeyIgnoringBAMOutputFormat }
import htsjdk.samtools.SAMFileHeader
import hbparquet.hadoop.util.ContextUtil
import org.apache.hadoop.fs.Path
import org.apache.hadoop.mapreduce.{ OutputFormat, RecordWriter, TaskAttemptContext }
import org.apache.spark.rdd.InstrumentedOutputFormat
import org.apache.hadoop.mapreduce.OutputFormat
import org.bdgenomics.adam.instrumentation.Timers
import org.seqdoop.hadoop_bam.{
KeyIgnoringBAMOutputFormat,
KeyIgnoringBAMRecordWriter,
SAMRecordWritable
}

object ADAMBAMOutputFormat extends Serializable {

Expand Down Expand Up @@ -76,11 +82,26 @@ class InstrumentedADAMBAMOutputFormat[K] extends InstrumentedOutputFormat[K, org
class ADAMBAMOutputFormatHeaderLess[K]
extends KeyIgnoringBAMOutputFormat[K] with Serializable {

setSAMHeader(ADAMBAMOutputFormat.getHeader)
setWriteHeader(false)

override def getRecordWriter(context: TaskAttemptContext): RecordWriter[K, SAMRecordWritable] = {
val conf = ContextUtil.getConfiguration(context)

// where is our header file?
val path = new Path(conf.get("org.bdgenomics.adam.rdd.read.bam_header_path"))

// read the header file
readSAMHeaderFrom(path, conf)

// now that we have the header set, we need to make a record reader
return new KeyIgnoringBAMRecordWriter[K](getDefaultWorkFile(context, ""),
header,
false,
context)
}
}

class InstrumentedADAMBAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, org.seqdoop.hadoop_bam.SAMRecordWritable] {
override def timerName(): String = Timers.WriteBAMRecord.timerName
override def outputFormatClass(): Class[_ <: OutputFormat[K, SAMRecordWritable]] = classOf[ADAMBAMOutputFormatHeaderLess[K]]
}
}
27 changes: 24 additions & 3 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMSAMOutputFormat.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,18 @@
*/
package org.bdgenomics.adam.rdd.read

import org.seqdoop.hadoop_bam.{ SAMRecordWritable, KeyIgnoringAnySAMOutputFormat, SAMFormat }
import htsjdk.samtools.SAMFileHeader
import hbparquet.hadoop.util.ContextUtil
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.apache.hadoop.mapreduce.OutputFormat
import org.seqdoop.hadoop_bam.{
KeyIgnoringAnySAMOutputFormat,
KeyIgnoringSAMRecordWriter,
SAMFormat,
SAMRecordWritable
}

object ADAMSAMOutputFormat extends Serializable {

Expand Down Expand Up @@ -76,9 +83,23 @@ class InstrumentedADAMSAMOutputFormat[K] extends InstrumentedOutputFormat[K, org
class ADAMSAMOutputFormatHeaderLess[K]
extends KeyIgnoringAnySAMOutputFormat[K](SAMFormat.valueOf("SAM")) with Serializable {

setSAMHeader(ADAMSAMOutputFormat.getHeader)
setWriteHeader(false)

override def getRecordWriter(context: TaskAttemptContext): RecordWriter[K, SAMRecordWritable] = {
val conf = ContextUtil.getConfiguration(context)

// where is our header file?
val path = new Path(conf.get("org.bdgenomics.adam.rdd.read.bam_header_path"))

// read the header file
readSAMHeaderFrom(path, conf)

// now that we have the header set, we need to make a record reader
return new KeyIgnoringSAMRecordWriter(getDefaultWorkFile(context, ""),
header,
false,
context)
}
}

class InstrumentedADAMSAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, org.seqdoop.hadoop_bam.SAMRecordWritable] {
Expand Down
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