0.23.1

hammerlab · Jun 20, 2017 · f93b20b · f93b20b
1 parent b61fdd5
commit f93b20b
Show file tree

Hide file tree

Showing 7 changed files with 25 additions and 20 deletions.
diff --git a/build.sbt b/build.sbt
@@ -2,7 +2,7 @@ organization := "org.hammerlab.adam"
 
 name := sparkName("core")
 
-version := "0.23.1-SNAPSHOT"
+version := "0.23.1"
 
 addSparkDeps
 publishTestJar
@@ -20,7 +20,7 @@ deps ++= Seq(
   libs.value('bdg_utils_metrics),
   libs.value('bdg_utils_misc),
   libs.value('commons_io),
-  libs.value('hadoop_bam),
+  "org.seqdoop" % "hadoop-bam" % "7.8.0" exclude("org.apache.hadoop", "hadoop-client"),
   libs.value('htsjdk),
   libs.value('loci),
   libs.value('log4j),

diff --git a/project/plugins.sbt b/project/plugins.sbt
@@ -1 +1 @@
-addSbtPlugin("org.hammerlab" % "sbt-parent" % "1.7.7-SNAPSHOT")
+addSbtPlugin("org.hammerlab" % "sbt-parent" % "2.0.1")
diff --git a/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala b/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala
@@ -91,7 +91,7 @@ class ADAMContextSuite
   test("can read a small .CRAM file") {
     val path = testFile("artificial.cram")
     val referencePath = resourceUrl("artificial.fa").toString
-    sc.hadoopConfiguration.set(REFERENCE_SOURCE_PATH_PROPERTY,
+    hadoopConf.set(REFERENCE_SOURCE_PATH_PROPERTY,
       referencePath)
     val reads: RDD[AlignmentRecord] = sc.loadAlignments(path).rdd
     reads.count() should === (10)

diff --git a/src/test/scala/org/bdgenomics/adam/rdd/ParallelFileMergerSuite.scala b/src/test/scala/org/bdgenomics/adam/rdd/ParallelFileMergerSuite.scala
@@ -21,7 +21,7 @@ import org.apache.hadoop.fs.{ FileSystem, Path }
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ParallelFileMerger._
 import org.bdgenomics.adam.util.ADAMFunSuite
-import org.seqdoop.hadoop_bam.CRAMInputFormat
+import org.seqdoop.hadoop_bam.CRAMInputFormat.REFERENCE_SOURCE_PATH_PROPERTY
 
 class ParallelFileMergerSuite
   extends ADAMFunSuite {
@@ -63,7 +63,7 @@ class ParallelFileMergerSuite
 
     val fileSizes = Seq(29408, 3093)
 
-    val fs = FileSystem.get(sc.hadoopConfiguration)
+    val fs = FileSystem.get(hadoopConf)
     val (size, sizes) = getFullSize(fs, files)
 
     assert(size === fileSizes.sum.toLong)
@@ -93,7 +93,7 @@ class ParallelFileMergerSuite
       )
       .map(new Path(_))
 
-    val fs = FileSystem.get(sc.hadoopConfiguration)
+    val fs = FileSystem.get(hadoopConf)
     val fileSizesMap =
       files
         .map(f ⇒ (f, fs.getFileStatus(f).getLen().toInt))
@@ -127,7 +127,7 @@ class ParallelFileMergerSuite
     )
     .map(new Path(_))
 
-    val fs = FileSystem.get(sc.hadoopConfiguration)
+    val fs = FileSystem.get(hadoopConf)
     val fileSizesMap =
       files
         .map(f ⇒ (f, fs.getFileStatus(f).getLen().toInt))
@@ -173,7 +173,7 @@ class ParallelFileMergerSuite
     reads.transform(_.repartition(4))
       .saveAsSam(outPath, asSingleFile = true, deferMerging = true)
 
-    val fs = FileSystem.get(sc.hadoopConfiguration)
+    val fs = FileSystem.get(hadoopConf)
     val filesToMerge = (Seq(outPath + "_head") ++ (0 until 4).map(i => {
       (outPath + "_tail") / "part-r-0000%d".format(i)
     })).map(new Path(_))
@@ -182,7 +182,7 @@ class ParallelFileMergerSuite
     mergePaths(
       outPath,
       filesToMerge,
-      sc.broadcast(sc.hadoopConfiguration),
+      sc.broadcast(hadoopConf),
       false,
       false
     )
@@ -199,7 +199,7 @@ class ParallelFileMergerSuite
     reads.transform(_.repartition(4))
       .saveAsSam(outPath, asSingleFile = true, deferMerging = true)
 
-    val fs = FileSystem.get(sc.hadoopConfiguration)
+    val fs = FileSystem.get(hadoopConf)
     val filesToMerge = (Seq(outPath + "_head") ++ (0 until 4).map(i => {
       (outPath + "_tail") / "part-r-0000%d".format(i)
     })).map(new Path(_))
@@ -208,7 +208,7 @@ class ParallelFileMergerSuite
     mergePaths(
       outPath,
       filesToMerge,
-      sc.broadcast(sc.hadoopConfiguration),
+      sc.broadcast(hadoopConf),
       true,
       false
     )
@@ -220,15 +220,17 @@ class ParallelFileMergerSuite
 
   test("merge a sharded cram file") {
     val referencePath = resourceUrl("artificial.fa").toString
-    sc.hadoopConfiguration.set(CRAMInputFormat.REFERENCE_SOURCE_PATH_PROPERTY,
-      referencePath)
+    hadoopConf.set(
+      REFERENCE_SOURCE_PATH_PROPERTY,
+      referencePath
+    )
     val reads = sc.loadAlignments(testFile("artificial.cram"))
     val outPath = tmpFile("out.cram")
 
     reads.transform(_.repartition(4))
       .saveAsSam(outPath, isSorted = true, asSingleFile = true, deferMerging = true)
 
-    val fs = FileSystem.get(sc.hadoopConfiguration)
+    val fs = FileSystem.get(hadoopConf)
     val filesToMerge = (Seq(outPath + "_head") ++ (0 until 4).map(i => {
       (outPath + "_tail") / "part-r-0000%d".format(i)
     })).map(new Path(_))
@@ -237,7 +239,7 @@ class ParallelFileMergerSuite
     mergePaths(
       outPath,
       filesToMerge,
-      sc.broadcast(sc.hadoopConfiguration),
+      sc.broadcast(hadoopConf),
       false,
       true
     )

diff --git a/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDSuite.scala b/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDSuite.scala
@@ -25,7 +25,7 @@ class FragmentRDDSuite extends ADAMFunSuite {
 
   test("don't lose any reads when piping interleaved fastq to sam") {
     // write suffixes at end of reads
-    sc.hadoopConfiguration.setBoolean(InterleavedFASTQInFormatter.WRITE_SUFFIXES, true)
+    hadoopConf.setBoolean(InterleavedFASTQInFormatter.WRITE_SUFFIXES, true)
 
     val fragmentsPath = testFile("interleaved_fastq_sample1.ifq")
     val ardd = sc.loadFragments(fragmentsPath)

diff --git a/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala b/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala
@@ -217,7 +217,7 @@ class AlignmentRecordRDDSuite
   test("round trip with single CRAM file produces equivalent Read values") {
     val readsPath = testFile("artificial.cram")
     val referencePath = resourceUrl("artificial.fa").toString
-    sc.hadoopConfiguration.set(REFERENCE_SOURCE_PATH_PROPERTY,
+    hadoopConf.set(REFERENCE_SOURCE_PATH_PROPERTY,
       referencePath)
 
     val ardd = sc.loadBam(readsPath)
@@ -250,7 +250,7 @@ class AlignmentRecordRDDSuite
   test("round trip with sharded CRAM file produces equivalent Read values") {
     val readsPath = testFile("artificial.cram")
     val referencePath = resourceUrl("artificial.fa").toString
-    sc.hadoopConfiguration.set(REFERENCE_SOURCE_PATH_PROPERTY,
+    hadoopConf.set(REFERENCE_SOURCE_PATH_PROPERTY,
       referencePath)
 
     val ardd = sc.loadBam(readsPath)

diff --git a/src/test/scala/org/bdgenomics/adam/util/ADAMFunSuite.scala b/src/test/scala/org/bdgenomics/adam/util/ADAMFunSuite.scala
@@ -29,7 +29,10 @@ import org.hammerlab.test.resources.{ File, Url }
 import org.scalactic.TypeCheckedTripleEquals
 
 abstract class ADAMFunSuite
-  extends KryoSparkSuite(classOf[ADAMKryoRegistrator], referenceTracking = true)
+  extends KryoSparkSuite(
+    classOf[ADAMKryoRegistrator],
+    referenceTracking = true
+  )
     with ContigNameCanEqualString
     with LocusCanEqualInt
     with ClearContigNames