Merge 372b573 into 10ec74e

.gitignore

@@ -11,4 +11,4 @@ build
 .*.swp
 .DS_Store
 
-*#*
+*#*

adam-apis/pom.xml

@@ -26,7 +26,7 @@
         <groupId>org.scalatest</groupId>
         <artifactId>scalatest-maven-plugin</artifactId>
         <configuration>
-          <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
+          <reportsDirectory>${project.build.directory}/scalatest-reports</reportsDirectory>
           <junitxml>.</junitxml>
           <filereports>ADAMTestSuite.txt</filereports>
           <!--

adam-cli/pom.xml

@@ -53,7 +53,7 @@
         <groupId>org.scalatest</groupId>
         <artifactId>scalatest-maven-plugin</artifactId>
         <configuration>
-          <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
+          <reportsDirectory>${project.build.directory}/scalatest-reports</reportsDirectory>
           <junitxml>.</junitxml>
           <filereports>ADAMTestSuite.txt</filereports>
           <!--

adam-cli/src/test/scala/org/bdgenomics/adam/cli/ADAM2FastqSuite.scala

@@ -27,7 +27,7 @@ import org.bdgenomics.formats.avro.AlignmentRecord
 class Adam2FastqSuite extends ADAMFunSuite {
 
   sparkTest("convert SAM to paired FASTQ") {
-    val readsFilepath = resourcePath("bqsr1.sam")
+    val readsFilepath = testFile("bqsr1.sam")
 
     // The following fastq files were generated by Picard's SamToFastq
 
@@ -45,8 +45,8 @@ class Adam2FastqSuite extends ADAMFunSuite {
 
     // VALIDATION_STRINGENCY=SILENT is necessary since they are unpaired reads and this matches the ADAM default
 
-    val fastq1Path = resourcePath("bqsr1-r1.fq")
-    val fastq2Path = resourcePath("bqsr1-r2.fq")
+    val fastq1Path = testFile("bqsr1-r1.fq")
+    val fastq2Path = testFile("bqsr1-r2.fq")
 
     val outputDir = Files.createTempDir()
     val outputFastqR1File = outputDir.getAbsolutePath + "/bqsr1-r1.fq"

adam-cli/src/test/scala/org/bdgenomics/adam/cli/FlagStatSuite.scala

@@ -30,7 +30,7 @@ class FlagStatSuite extends ADAMFunSuite {
 
   sparkTest("Standard FlagStat test") {
 
-    val inputpath = resourcePath("NA12878.sam")
+    val inputpath = testFile("NA12878.sam")
     val argLine = "%s".format(inputpath).split("\\s+")
 
     val args: FlagStatArgs = Args4j.apply[FlagStatArgs](argLine)

adam-core/pom.xml

@@ -26,7 +26,7 @@
         <groupId>org.scalatest</groupId>
         <artifactId>scalatest-maven-plugin</artifactId>
         <configuration>
-          <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
+          <reportsDirectory>${project.build.directory}/scalatest-reports</reportsDirectory>
           <junitxml>.</junitxml>
           <filereports>ADAMTestSuite.txt</filereports>
           <!--

adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromReadsSuite.scala

@@ -28,7 +28,7 @@ class ConsensusGeneratorFromReadsSuite extends ADAMFunSuite {
   val cg = new ConsensusGeneratorFromReads
 
   def artificial_reads: RDD[AlignmentRecord] = {
-    val path = resourcePath("artificial.sam")
+    val path = testFile("artificial.sam")
     sc.loadAlignments(path).rdd
   }
 

adam-core/src/test/scala/org/bdgenomics/adam/converters/FastaConverterSuite.scala

@@ -206,7 +206,7 @@ class FastaConverterSuite extends ADAMFunSuite {
     assert(convertedFragmentSequence2 === fastaFragmentSequence2)
   }
 
-  val chr1File = resourcePath("human_g1k_v37_chr1_59kb.fasta")
+  val chr1File = testFile("human_g1k_v37_chr1_59kb.fasta")
 
   sparkTest("convert reference fasta file") {
     //Loading "human_g1k_v37_chr1_59kb.fasta"

adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala

@@ -28,7 +28,7 @@ import scala.collection.JavaConversions._
 
 class VariantContextConverterSuite extends ADAMFunSuite {
   val dictionary = {
-    val path = resourcePath("dict_with_accession.dict")
+    val path = testFile("dict_with_accession.dict")
     SequenceDictionary(SAMFileReader.getSequenceDictionary(new File(path)))
   }
 

adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala

@@ -41,7 +41,7 @@ class SequenceDictionarySuite extends ADAMFunSuite {
   }
 
   test("Convert from SAM sequence dictionary file (with extra fields)") {
-    val path = resourcePath("dict_with_accession.dict")
+    val path = testFile("dict_with_accession.dict")
     val ssd = SAMFileReader.getSequenceDictionary(new File(path))
 
     val chr1 = ssd.getSequence("1") // Validate that extra fields are parsed
@@ -55,7 +55,7 @@ class SequenceDictionarySuite extends ADAMFunSuite {
   }
 
   test("merge into existing dictionary") {
-    val path = resourcePath("dict_with_accession.dict")
+    val path = testFile("dict_with_accession.dict")
     val ssd = SAMFileReader.getSequenceDictionary(new File(path))
 
     val asd = SequenceDictionary(ssd)
@@ -68,7 +68,7 @@ class SequenceDictionarySuite extends ADAMFunSuite {
   }
 
   test("Convert from SAM sequence dictionary and back") {
-    val path = resourcePath("dict_with_accession.dict")
+    val path = testFile("dict_with_accession.dict")
     val ssd = SAMFileReader.getSequenceDictionary(new File(path))
     val asd = SequenceDictionary(ssd)
     ssd.assertSameDictionary(SequenceDictionary.toSAMSequenceDictionary(asd))
@@ -212,7 +212,7 @@ class SequenceDictionarySuite extends ADAMFunSuite {
   }
 
   test("load sequence dictionary from VCF file") {
-    val path = resourcePath("small.vcf")
+    val path = testFile("small.vcf")
     val fileReader = new VCFFileReader(new File(path), false)
     val sd = SequenceDictionary.fromVCFHeader(fileReader.getFileHeader)
 

adam-core/src/test/scala/org/bdgenomics/adam/projections/FieldEnumerationSuite.scala

@@ -34,7 +34,7 @@ class FieldEnumerationSuite extends ADAMFunSuite {
   }
 
   sparkTest("Simple projection on Read works") {
-    val readsFilepath = resourcePath("reads12.sam")
+    val readsFilepath = testFile("reads12.sam")
     val readsParquetFilepath = tmpFile("reads12.adam")
 
     // Convert the reads12.sam file into a parquet file

adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala

@@ -47,7 +47,7 @@ case class TestSaveArgs(var outputPath: String) extends ADAMSaveAnyArgs {
 class ADAMContextSuite extends ADAMFunSuite {
 
   sparkTest("sc.loadParquet should not fail on unmapped reads") {
-    val readsFilepath = resourcePath("unmapped.sam")
+    val readsFilepath = testFile("unmapped.sam")
 
     // Convert the reads12.sam file into a parquet file
     val bamReads: RDD[AlignmentRecord] = sc.loadAlignments(readsFilepath).rdd
@@ -58,7 +58,7 @@ class ADAMContextSuite extends ADAMFunSuite {
     //load an existing file from the resources and save it as an ADAM file.
     //This way we are not dependent on the ADAM format (as we would if we used a pre-made ADAM file)
     //but we are dependent on the unmapped.sam file existing, maybe I should make a new one
-    val readsFilepath = resourcePath("unmapped.sam")
+    val readsFilepath = testFile("unmapped.sam")
     val bamReads = sc.loadAlignments(readsFilepath)
     //save it as an Adam file so we can test the Adam loader
     val bamReadsAdamFile = new File(Files.createTempDir(), "bamReads.adam")
@@ -72,19 +72,19 @@ class ADAMContextSuite extends ADAMFunSuite {
   }
 
   sparkTest("can read a small .SAM file") {
-    val path = resourcePath("small.sam")
+    val path = testFile("small.sam")
     val reads: RDD[AlignmentRecord] = sc.loadAlignments(path).rdd
     assert(reads.count() === 20)
   }
 
   sparkTest("can read a small .SAM with all attribute tag types") {
-    val path = resourcePath("tags.sam")
+    val path = testFile("tags.sam")
     val reads: RDD[AlignmentRecord] = sc.loadAlignments(path).rdd
     assert(reads.count() === 7)
   }
 
   sparkTest("can filter a .SAM file based on quality") {
-    val path = resourcePath("small.sam")
+    val path = testFile("small.sam")
     val reads: RDD[AlignmentRecord] = sc.loadAlignments(path)
       .rdd
       .filter(a => (a.getReadMapped && a.getMapq > 30))
@@ -251,7 +251,7 @@ class ADAMContextSuite extends ADAMFunSuite {
   }
 
   sparkTest("can read a small .vcf file") {
-    val path = resourcePath("small.vcf")
+    val path = testFile("small.vcf")
 
     val vcs = sc.loadGenotypes(path).toVariantContextRDD.rdd.collect.sortBy(_.position)
     assert(vcs.size === 5)
@@ -265,44 +265,44 @@ class ADAMContextSuite extends ADAMFunSuite {
   }
 
   sparkTest("can read a gzipped .vcf file") {
-    val path = resourcePath("test.vcf.gz")
+    val path = testFile("test.vcf.gz")
     val vcs = sc.loadVcf(path)
     assert(vcs.rdd.count === 6)
   }
 
   sparkTest("can read a BGZF gzipped .vcf file with .gz file extension") {
-    val path = resourcePath("test.vcf.bgzf.gz")
+    val path = testFile("test.vcf.bgzf.gz")
     val vcs = sc.loadVcf(path)
     assert(vcs.rdd.count === 6)
   }
 
   sparkTest("can read a BGZF gzipped .vcf file with .bgz file extension") {
-    val path = resourcePath("test.vcf.bgz")
+    val path = testFile("test.vcf.bgz")
     val vcs = sc.loadVcf(path)
     assert(vcs.rdd.count === 6)
   }
 
   ignore("can read an uncompressed BCFv2.2 file") { // see https://github.com/samtools/htsjdk/issues/507
-    val path = resourcePath("test.uncompressed.bcf")
+    val path = testFile("test.uncompressed.bcf")
     val vcs = sc.loadVcf(path)
     assert(vcs.rdd.count === 6)
   }
 
   ignore("can read a BGZF compressed BCFv2.2 file") { // see https://github.com/samtools/htsjdk/issues/507
-    val path = resourcePath("test.compressed.bcf")
+    val path = testFile("test.compressed.bcf")
     val vcs = sc.loadVcf(path)
     assert(vcs.rdd.count === 6)
   }
 
   sparkTest("loadIndexedVcf with 1 ReferenceRegion") {
-    val path = resourcePath("bqsr1.vcf")
+    val path = testFile("bqsr1.vcf")
     val refRegion = ReferenceRegion("22", 16097644, 16098647)
     val vcs = sc.loadIndexedVcf(path, refRegion)
     assert(vcs.rdd.count == 17)
   }
 
   sparkTest("loadIndexedVcf with multiple ReferenceRegions") {
-    val path = resourcePath("bqsr1.vcf")
+    val path = testFile("bqsr1.vcf")
     val refRegion1 = ReferenceRegion("22", 16050678, 16050822)
     val refRegion2 = ReferenceRegion("22", 16097644, 16098647)
     val vcs = sc.loadIndexedVcf(path, Iterable(refRegion1, refRegion2))
@@ -311,7 +311,7 @@ class ADAMContextSuite extends ADAMFunSuite {
 
   (1 to 4) foreach { testNumber =>
     val inputName = "interleaved_fastq_sample%d.ifq".format(testNumber)
-    val path = ClassLoader.getSystemClassLoader.getResource(inputName).getFile
+    val path = testFile(inputName)
 
     sparkTest("import records from interleaved FASTQ: %d".format(testNumber)) {
 
@@ -335,7 +335,7 @@ class ADAMContextSuite extends ADAMFunSuite {
 
   (1 to 4) foreach { testNumber =>
     val inputName = "fastq_sample%d.fq".format(testNumber)
-    val path = ClassLoader.getSystemClassLoader.getResource(inputName).getFile
+    val path = testFile(inputName)
 
     sparkTest("import records from single ended FASTQ: %d".format(testNumber)) {
 
@@ -357,7 +357,7 @@ class ADAMContextSuite extends ADAMFunSuite {
   }
 
   sparkTest("filter on load using the filter2 API") {
-    val path = resourcePath("bqsr1.vcf")
+    val path = testFile("bqsr1.vcf")
 
     val variants = sc.loadVariants(path)
     assert(variants.rdd.count === 681)
@@ -372,7 +372,7 @@ class ADAMContextSuite extends ADAMFunSuite {
   }
 
   sparkTest("saveAsParquet with file path") {
-    val inputPath = resourcePath("small.sam")
+    val inputPath = testFile("small.sam")
     val reads = sc.loadAlignments(inputPath)
     val outputPath = tmpLocation()
     reads.saveAsParquet(outputPath)
@@ -381,7 +381,7 @@ class ADAMContextSuite extends ADAMFunSuite {
   }
 
   sparkTest("saveAsParquet with file path, block size, page size") {
-    val inputPath = resourcePath("small.sam")
+    val inputPath = testFile("small.sam")
     val reads = sc.loadAlignments(inputPath)
     val outputPath = tmpLocation()
     reads.saveAsParquet(outputPath, 1024, 2048)
@@ -390,7 +390,7 @@ class ADAMContextSuite extends ADAMFunSuite {
   }
 
   sparkTest("saveAsParquet with save args") {
-    val inputPath = resourcePath("small.sam")
+    val inputPath = testFile("small.sam")
     val reads = sc.loadAlignments(inputPath)
     val outputPath = tmpLocation()
     reads.saveAsParquet(TestSaveArgs(outputPath))
@@ -399,7 +399,7 @@ class ADAMContextSuite extends ADAMFunSuite {
   }
 
   sparkTest("read a gzipped fasta file") {
-    val inputPath = resourcePath("chr20.250k.fa.gz")
+    val inputPath = testFile("chr20.250k.fa.gz")
     val contigFragments: RDD[NucleotideContigFragment] = sc.loadFasta(inputPath, 10000L)
       .rdd
       .sortBy(_.getFragmentNumber.toInt)
@@ -422,15 +422,15 @@ class ADAMContextSuite extends ADAMFunSuite {
 
   sparkTest("loadIndexedBam with 1 ReferenceRegion") {
     val refRegion = ReferenceRegion("chr2", 100, 101)
-    val path = resourcePath("sorted.bam")
+    val path = testFile("sorted.bam")
     val reads = sc.loadIndexedBam(path, refRegion)
     assert(reads.rdd.count == 1)
   }
 
   sparkTest("loadIndexedBam with multiple ReferenceRegions") {
     val refRegion1 = ReferenceRegion("chr2", 100, 101)
     val refRegion2 = ReferenceRegion("3", 10, 17)
-    val path = resourcePath("sorted.bam")
+    val path = testFile("sorted.bam")
     val reads = sc.loadIndexedBam(path, Iterable(refRegion1, refRegion2))
     assert(reads.rdd.count == 2)
   }

adam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicPositionPartitionerSuite.scala

@@ -94,7 +94,7 @@ class GenomicPositionPartitionerSuite extends ADAMFunSuite {
   }
 
   sparkTest("test that simple partitioning works okay on a reasonable set of ADAMRecords") {
-    val filename = resourcePath("reads12.sam")
+    val filename = testFile("reads12.sam")
     val parts = 1
 
     val dict = sc.loadDictionary[AlignmentRecord](filename)