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[ADAM-1486] Respect validation stringency if BAM header load fails. #1525

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merged 1 commit into from May 16, 2017
Merged

[ADAM-1486] Respect validation stringency if BAM header load fails. #1525

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10 changes: 7 additions & 3 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
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Expand Up @@ -595,9 +595,13 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
Some((sd, rg))
} catch {
case e: Throwable => {
log.error(
s"Loading failed for $fp:n${e.getMessage}\n\t${e.getStackTrace.take(25).map(_.toString).mkString("\n\t")}"
)
if (validationStringency == ValidationStringency.STRICT) {
throw e
} else if (validationStringency == ValidationStringency.LENIENT) {
log.error(
s"Loading failed for $fp:\n${e.getMessage}\n\t${e.getStackTrace.take(25).map(_.toString).mkString("\n\t")}"
)
}
None
}
}
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3 changes: 3 additions & 0 deletions adam-core/src/test/resources/badheader.sam
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@@ -0,0 +1,3 @@
@SQ SNN:1 LN:249250621
@SQ SN:2 LN:243199373
simread:1:26472783:false 16 1 26472784 60 75M * 0 0 GTATAAGAGCAGCCTTATTCCTATTTATAATCAGGGTGAAACACCTGTGCCAATGCCAAGACAGGGGTGCCAAGA * NM:i:0 AS:i:75 XS:i:0
8 changes: 8 additions & 0 deletions adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala
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Expand Up @@ -17,6 +17,7 @@
*/
package org.bdgenomics.adam.rdd

import htsjdk.samtools.{ SAMFormatException, ValidationStringency }
import java.io.{ File, FileNotFoundException }
import com.google.common.io.Files
import org.apache.hadoop.fs.Path
Expand Down Expand Up @@ -81,6 +82,13 @@ class ADAMContextSuite extends ADAMFunSuite {
assert(reads.count() === 20)
}

sparkTest("loading a sam file with a bad header and strict stringency should fail") {
val path = testFile("badheader.sam")
intercept[SAMFormatException] {
sc.loadBam(path, validationStringency = ValidationStringency.STRICT)
}
}

sparkTest("can read a small .CRAM file") {
val path = testFile("artificial.cram")
val referencePath = resourceUrl("artificial.fa").toString
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