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random nits #437

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random nits #437

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3 changes: 2 additions & 1 deletion adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
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Expand Up @@ -219,7 +219,8 @@ class ADAMContext(val sc: SparkContext) extends Serializable with Logging {
} else {
reads
}
} else if ((filePath.endsWith(".fastq") || filePath.endsWith(".fq")) && classOf[AlignmentRecord].isAssignableFrom(manifest[T].runtimeClass)) {
} else if ((filePath.endsWith(".fastq") || filePath.endsWith(".fq")) &&
classOf[AlignmentRecord].isAssignableFrom(manifest[T].runtimeClass)) {

if (projection.isDefined) {
log.warn("Projection is ignored when loading a FASTQ file")
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9 changes: 8 additions & 1 deletion adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordContext.scala
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Expand Up @@ -92,6 +92,13 @@ object AlignmentRecordContext extends Serializable with Logging {

class AlignmentRecordContext(val sc: SparkContext) extends Serializable with Logging {

/**
* Load AlignmentRecords from two paired-end FASTQ files.
*
* @param firstPairPath Path to read first-mates from
* @param secondPairPath Path to read second-mates from
* @param fixPairs Iff true, joins the first- and second-reads around their read name (minus the /1 or /2 suffix)
*/
def adamFastqLoad(firstPairPath: String,
secondPairPath: String,
fixPairs: Boolean = false): RDD[AlignmentRecord] = {
Expand Down Expand Up @@ -119,7 +126,7 @@ class AlignmentRecordContext(val sc: SparkContext) extends Serializable with Log
.build())
} else {
// all paired end reads should have the same name, except for the last two
// characters, which will be _1/_2
// characters, which will be {/1, /2}
firstPairRdd.keyBy(_.getReadName.toString.dropRight(2)).join(secondPairRdd.keyBy(_.getReadName.toString.dropRight(2)))
.flatMap(kv => Seq(AlignmentRecord.newBuilder(kv._2._1)
.setReadPaired(true)
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18 changes: 16 additions & 2 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala
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Expand Up @@ -87,8 +87,22 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
// write file to disk
val conf = rdd.context.hadoopConfiguration
asSam match {
case true => withKey.saveAsNewAPIHadoopFile(filePath, classOf[LongWritable], classOf[SAMRecordWritable], classOf[ADAMSAMOutputFormat[LongWritable]], conf)
case false => withKey.saveAsNewAPIHadoopFile(filePath, classOf[LongWritable], classOf[SAMRecordWritable], classOf[ADAMBAMOutputFormat[LongWritable]], conf)
case true =>
withKey.saveAsNewAPIHadoopFile(
filePath,
classOf[LongWritable],
classOf[SAMRecordWritable],
classOf[ADAMSAMOutputFormat[LongWritable]],
conf
)
case false =>
withKey.saveAsNewAPIHadoopFile(
filePath,
classOf[LongWritable],
classOf[SAMRecordWritable],
classOf[ADAMBAMOutputFormat[LongWritable]],
conf
)
}
}

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1 change: 1 addition & 0 deletions pom.xml
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Expand Up @@ -283,6 +283,7 @@
<alignParameters>true</alignParameters>
<alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
<doubleIndentClassDeclaration>true</doubleIndentClassDeclaration>
<preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
</configuration>
</execution>
</executions>
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