misc pom/test/resource improvements

.gitignore

@@ -5,10 +5,11 @@ adam*.jar
 build
 *~
 #*
+*.bak
 *.bam*
 *.adam*
 *.log
 .*.swp
 .DS_Store
 
-*#*
+*#*

adam-apis/pom.xml

@@ -10,7 +10,7 @@
 
   <artifactId>adam-apis_2.10</artifactId>
   <packaging>jar</packaging>
-  <name>ADAM_2.10: APIs for Java</name>
+  <name>ADAM_${scala.version.prefix}: APIs for Java</name>
   <build>
     <plugins>
       <!-- disable surefire -->
@@ -26,7 +26,7 @@
         <groupId>org.scalatest</groupId>
         <artifactId>scalatest-maven-plugin</artifactId>
         <configuration>
-          <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
+          <reportsDirectory>${project.build.directory}/scalatest-reports</reportsDirectory>
           <junitxml>.</junitxml>
           <filereports>ADAMTestSuite.txt</filereports>
           <!--
@@ -100,11 +100,11 @@
     </dependency>
     <dependency>
       <groupId>org.apache.spark</groupId>
-      <artifactId>spark-core_2.10</artifactId>
+      <artifactId>spark-core_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc_2.10</artifactId>
+      <artifactId>utils-misc_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
@@ -114,11 +114,11 @@
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-core_2.10</artifactId>
+      <artifactId>adam-core_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-core_2.10</artifactId>
+      <artifactId>adam-core_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
@@ -132,7 +132,7 @@
     </dependency>
     <dependency>
       <groupId>org.scalatest</groupId>
-      <artifactId>scalatest_2.10</artifactId>
+      <artifactId>scalatest_${scala.version.prefix}</artifactId>
       <scope>test</scope>
     </dependency>
   </dependencies>

adam-assembly/pom.xml

@@ -10,13 +10,13 @@
 
   <artifactId>adam-assembly_2.10</artifactId>
   <packaging>jar</packaging>
-  <name>ADAM_2.10: Assembly</name>
+  <name>ADAM_${scala.version.prefix}: Assembly</name>
   <properties>
     <timestamp>${maven.build.timestamp}</timestamp>
     <maven.build.timestamp.format>yyyy-MM-dd</maven.build.timestamp.format>
   </properties>
   <build>
-    <finalName>adam_2.10-${project.version}</finalName>
+    <finalName>adam_${scala.version.prefix}-${project.version}</finalName>
     <plugins>
       <plugin>
         <groupId>org.codehaus.mojo</groupId>
@@ -114,7 +114,7 @@
   <dependencies>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-cli_2.10</artifactId>
+      <artifactId>adam-cli_${scala.version.prefix}</artifactId>
     </dependency>
   </dependencies>
 </project>

adam-cli/pom.xml

@@ -10,7 +10,7 @@
 
   <artifactId>adam-cli_2.10</artifactId>
   <packaging>jar</packaging>
-  <name>ADAM_2.10: CLI</name>
+  <name>ADAM_${scala.version.prefix}: CLI</name>
   <properties>
     <timestamp>${maven.build.timestamp}</timestamp>
     <maven.build.timestamp.format>yyyy-MM-dd</maven.build.timestamp.format>
@@ -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>
           <!--
@@ -111,51 +111,51 @@
     </dependency>
     <dependency>
       <groupId>org.apache.spark</groupId>
-      <artifactId>spark-core_2.10</artifactId>
+      <artifactId>spark-core_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc_2.10</artifactId>
+      <artifactId>utils-misc_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc_2.10</artifactId>
+      <artifactId>utils-misc_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-io_2.10</artifactId>
+      <artifactId>utils-io_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-cli_2.10</artifactId>
+      <artifactId>utils-cli_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-metrics_2.10</artifactId>
+      <artifactId>utils-metrics_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.bdg-formats</groupId>
       <artifactId>bdg-formats</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-core_2.10</artifactId>
+      <artifactId>adam-core_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-core_2.10</artifactId>
+      <artifactId>adam-core_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-apis_2.10</artifactId>
+      <artifactId>adam-apis_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-apis_2.10</artifactId>
+      <artifactId>adam-apis_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
@@ -173,12 +173,12 @@
     </dependency>
     <dependency>
       <groupId>org.scalatest</groupId>
-      <artifactId>scalatest_2.10</artifactId>
+      <artifactId>scalatest_${scala.version.prefix}</artifactId>
       <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>net.codingwell</groupId>
-      <artifactId>scala-guice_2.10</artifactId>
+      <artifactId>scala-guice_${scala.version.prefix}</artifactId>
     </dependency>
   </dependencies>
 </project>

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

@@ -10,7 +10,7 @@
 
   <artifactId>adam-core_2.10</artifactId>
   <packaging>jar</packaging>
-  <name>ADAM_2.10: Core</name>
+  <name>ADAM_${scala.version.prefix}: Core</name>
   <build>
     <plugins>
       <!-- disable surefire -->
@@ -26,7 +26,7 @@
         <groupId>org.scalatest</groupId>
         <artifactId>scalatest-maven-plugin</artifactId>
         <configuration>
-          <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
+          <reportsDirectory>${project.build.directory}/scalatest-reports</reportsDirectory>
           <junitxml>.</junitxml>
           <filereports>ADAMTestSuite.txt</filereports>
           <!--
@@ -92,25 +92,25 @@
   <dependencies>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc_2.10</artifactId>
+      <artifactId>utils-misc_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-metrics_2.10</artifactId>
+      <artifactId>utils-metrics_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-io_2.10</artifactId>
+      <artifactId>utils-io_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-cli_2.10</artifactId>
+      <artifactId>utils-cli_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-intervalrdd_2.10</artifactId>
+      <artifactId>utils-intervalrdd_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>com.esotericsoftware.kryo</groupId>
@@ -134,7 +134,7 @@
     </dependency>
     <dependency>
       <groupId>org.apache.spark</groupId>
-      <artifactId>spark-core_2.10</artifactId>
+      <artifactId>spark-core_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
       <groupId>it.unimi.dsi</groupId>
@@ -166,7 +166,7 @@
     </dependency>
     <dependency>
       <groupId>org.scalatest</groupId>
-      <artifactId>scalatest_2.10</artifactId>
+      <artifactId>scalatest_${scala.version.prefix}</artifactId>
       <scope>test</scope>
     </dependency>
     <dependency>

adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnowns.scala

@@ -37,7 +37,7 @@ import scala.transient
  * @param sc Spark context to use.
  */
 private[adam] class ConsensusGeneratorFromKnowns(file: String,
-                                                 @transient sc: SparkContext) extends ConsensusGenerator {
+                                                 sc: SparkContext) extends ConsensusGenerator {
 
   private val indelTable = sc.broadcast(IndelTable(file, sc))
 

adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala

@@ -26,7 +26,7 @@ object SAMFileHeaderWritable {
   }
 }
 
-class SAMFileHeaderWritable(@transient hdr: SAMFileHeader) extends Serializable {
+class SAMFileHeaderWritable(hdr: SAMFileHeader) extends Serializable {
   // extract fields that are needed in order to recreate the SAMFileHeader
   protected val text = {
     val txt: String = hdr.getTextHeader

adam-core/src/main/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoin.scala

@@ -29,7 +29,7 @@ sealed trait ShuffleRegionJoin[T, U, RT, RU] extends RegionJoin[T, U, RT, RU] {
 
   val sd: SequenceDictionary
   val partitionSize: Long
-  @transient val sc: SparkContext
+  val sc: SparkContext
 
   // Create the set of bins across the genome for parallel processing
   protected val seqLengths = Map(sd.records.toSeq.map(rec => (rec.name, rec.length)): _*)

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

@@ -40,7 +40,7 @@ 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
@@ -54,7 +54,7 @@ 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)
@@ -67,7 +67,7 @@ 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))
@@ -211,7 +211,7 @@ 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