Merge 065f6d7 into 6b28217

.travis.yml

@@ -1 +1,3 @@
 language: java
+jdk:
+  - oraclejdk8

adam-core/src/main/java/org/bdgenomics/adam/io/BAMFilteredRecordReader.scala

@@ -18,7 +18,6 @@
 
 package org.bdgenomics.adam.io
 
-import hbparquet.hadoop.util.ContextUtil
 import htsjdk.samtools.BAMRecordCodec
 import htsjdk.samtools.ValidationStringency
 import htsjdk.samtools.SAMRecord
@@ -72,7 +71,7 @@ class BAMFilteredRecordReader extends BAMRecordReader {
     }
     isInitialized = true
 
-    val conf: Configuration = ContextUtil.getConfiguration(ctx)
+    val conf: Configuration = ctx.getConfiguration()
 
     val split: FileVirtualSplit = spl.asInstanceOf[FileVirtualSplit]
     val file: Path = split.getPath()

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

@@ -56,7 +56,7 @@ import org.bdgenomics.utils.instrumentation.Metrics
 import org.bdgenomics.utils.io.LocalFileByteAccess
 import org.bdgenomics.utils.misc.HadoopUtil
 import org.seqdoop.hadoop_bam._
-import org.seqdoop.hadoop_bam.util.SAMHeaderReader
+import org.seqdoop.hadoop_bam.util.{ BGZFCodec, SAMHeaderReader }
 import scala.collection.JavaConversions._
 import scala.collection.Map
 import scala.reflect.ClassTag
@@ -578,6 +578,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
   def loadVcf(filePath: String, sd: Option[SequenceDictionary]): RDD[VariantContext] = {
     val job = HadoopUtil.newJob(sc)
     val vcc = new VariantContextConverter(sd)
+    job.getConfiguration().set("io.compression.codecs", classOf[BGZFCodec].getCanonicalName())
     val records = sc.newAPIHadoopFile(
       filePath,
       classOf[VCFInputFormat], classOf[LongWritable], classOf[VariantContextWritable],

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMBAMOutputFormat.scala

@@ -18,7 +18,6 @@
 package org.bdgenomics.adam.rdd.read
 
 import htsjdk.samtools.SAMFileHeader
-import hbparquet.hadoop.util.ContextUtil
 import org.apache.hadoop.fs.Path
 import org.apache.hadoop.mapreduce.{ OutputFormat, RecordWriter, TaskAttemptContext }
 import org.apache.spark.rdd.InstrumentedOutputFormat
@@ -85,7 +84,7 @@ class ADAMBAMOutputFormatHeaderLess[K]
   setWriteHeader(false)
 
   override def getRecordWriter(context: TaskAttemptContext): RecordWriter[K, SAMRecordWritable] = {
-    val conf = ContextUtil.getConfiguration(context)
+    val conf = context.getConfiguration()
 
     // where is our header file?
     val path = new Path(conf.get("org.bdgenomics.adam.rdd.read.bam_header_path"))

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMSAMOutputFormat.scala

@@ -18,7 +18,6 @@
 package org.bdgenomics.adam.rdd.read
 
 import htsjdk.samtools.SAMFileHeader
-import hbparquet.hadoop.util.ContextUtil
 import org.apache.hadoop.fs.Path
 import org.apache.hadoop.mapreduce.{ OutputFormat, RecordWriter, TaskAttemptContext }
 import org.apache.spark.rdd.InstrumentedOutputFormat
@@ -86,7 +85,7 @@ class ADAMSAMOutputFormatHeaderLess[K]
   setWriteHeader(false)
 
   override def getRecordWriter(context: TaskAttemptContext): RecordWriter[K, SAMRecordWritable] = {
-    val conf = ContextUtil.getConfiguration(context)
+    val conf = context.getConfiguration()
 
     // where is our header file?
     val path = new Path(conf.get("org.bdgenomics.adam.rdd.read.bam_header_path"))

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

@@ -281,6 +281,30 @@ class ADAMContextSuite extends ADAMFunSuite {
     assert(gt.getReadDepth === 20)
   }
 
+  sparkTest("can read a gzipped .vcf file") {
+    val path = resourcePath("test.vcf.gz")
+    val vcs = sc.loadVcf(path, None)
+    assert(vcs.count === 6)
+  }
+
+  sparkTest("can read a BGZF gzipped .vcf file") {
+    val path = resourcePath("test.vcf.bgzf.gz")
+    val vcs = sc.loadVcf(path, None)
+    assert(vcs.count === 6)
+  }
+
+  sparkTest("can read an uncompressed BCFv2.1 file") {
+    val path = resourcePath("test.uncompressed.bcf")
+    val vcs = sc.loadVcf(path, None)
+    assert(vcs.count === 6)
+  }
+
+  sparkTest("can read a BGZF compressed BCFv2.1 file") {
+    val path = resourcePath("test.compressed.bcf")
+    val vcs = sc.loadVcf(path, None)
+    assert(vcs.count === 6)
+  }
+
   (1 to 4) foreach { testNumber =>
     val inputName = "interleaved_fastq_sample%d.ifq".format(testNumber)
     val path = ClassLoader.getSystemClassLoader.getResource(inputName).getFile

pom.xml

@@ -17,17 +17,19 @@
   <url>http://bdgenomics.org/</url>
 
   <properties>
-    <java.version>1.7</java.version>
-    <avro.version>1.7.7</avro.version>
+    <java.version>1.8</java.version>
+    <avro.version>1.7.7</avro.version> <!-- note: 1.8.0 is available -->
     <!-- informative only, used in about template substitution -->
     <scala.version>2.10</scala.version>
     <spark.version>1.5.2</spark.version>
     <parquet.version>1.8.1</parquet.version>
     <!-- Edit the following line to configure the Hadoop (HDFS) version. -->
     <hadoop.version>2.6.0</hadoop.version>
+    <hadoop-bam.version>7.5.0-SNAPSHOT</hadoop-bam.version> <!-- note: currently builds against hadoop 2.2.0 -->
     <scoverage.version>1.1.1</scoverage.version>
+    <slf4j.version>1.7.21</slf4j.version>
     <utils.version>0.2.4</utils.version>
-    <htsjdk.version>1.139</htsjdk.version>
+    <htsjdk.version>2.2.1</htsjdk.version>
   </properties>
 
   <modules>
@@ -112,7 +114,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.3</version>
+          <version>3.5.1</version>
           <configuration>
             <source>${java.version}</source>
             <target>${java.version}</target>
@@ -140,8 +142,8 @@
                     <message>ADAM requires Maven 3.1.1 or greater</message>
                   </requireMavenVersion>
                   <requireJavaVersion>
-                    <version>[1.7,)</version>
-                    <message>ADAM requires Java 1.7 or greater</message>
+                    <version>[1.8,)</version>
+                    <message>ADAM requires Java 1.8 or greater</message>
                   </requireJavaVersion>
                 </rules>
               </configuration>
@@ -166,17 +168,17 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-shade-plugin</artifactId>
-          <version>2.4.1</version>
+          <version>2.4.3</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-surefire-plugin</artifactId>
-          <version>2.18.1</version>
+          <version>2.19.1</version>
         </plugin>
         <plugin>
           <groupId>org.codehaus.mojo</groupId>
           <artifactId>templating-maven-plugin</artifactId>
-          <version>1.0-alpha-3</version>
+          <version>1.0.0</version>
         </plugin>
         <plugin>
           <groupId>org.scalatest</groupId>
@@ -186,7 +188,7 @@
         <plugin>
           <groupId>pl.project13.maven</groupId>
           <artifactId>git-commit-id-plugin</artifactId>
-          <version>2.2.0</version>
+          <version>2.2.1</version>
           <configuration>
             <gitDescribe>
               <always>true</always>
@@ -222,7 +224,12 @@
         <plugin>
           <groupId>org.codehaus.mojo</groupId>
           <artifactId>build-helper-maven-plugin</artifactId>
-          <version>1.9.1</version>
+          <version>1.10</version>
+        </plugin>
+        <plugin>
+          <groupId>org.scalariform</groupId>
+          <artifactId>scalariform-maven-plugin</artifactId>
+          <version>0.1.4</version>
         </plugin>
       </plugins>
     </pluginManagement>
@@ -282,7 +289,6 @@
       <plugin>
         <groupId>org.scalariform</groupId>
         <artifactId>scalariform-maven-plugin</artifactId>
-        <version>0.1.4</version>
         <executions>
           <execution>
             <id>default-cli</id>
@@ -310,7 +316,7 @@
       </dependency>
       <dependency>
         <groupId>org.scoverage</groupId>
-        <artifactId>scalac-scoverage-plugin_2.10</artifactId>
+        <artifactId>scalac-scoverage-plugin_2.10</artifactId> <!-- note: this shows up as compile scope -->
         <version>${scoverage.version}</version>
       </dependency>
       <dependency>
@@ -463,7 +469,7 @@
       <dependency>
         <groupId>org.seqdoop</groupId>
         <artifactId>hadoop-bam</artifactId>
-        <version>7.1.0</version>
+        <version>${hadoop-bam.version}</version>
         <exclusions>
           <exclusion>
             <groupId>org.seqdoop</groupId>
@@ -484,23 +490,38 @@
       <dependency>
         <groupId>org.scalatest</groupId>
         <artifactId>scalatest_2.10</artifactId>
-        <version>2.2.5</version>
+        <version>2.2.6</version>
         <scope>test</scope>
       </dependency>
+      <dependency>
+        <groupId>org.slf4j</groupId>
+        <artifactId>jcl-over-slf4j</artifactId>
+        <version>${slf4j.version}</version>
+      </dependency>
+      <dependency>
+        <groupId>org.slf4j</groupId>
+        <artifactId>jul-to-slf4j</artifactId>
+        <version>${slf4j.version}</version>
+      </dependency>
+      <dependency>
+        <groupId>org.slf4j</groupId>
+        <artifactId>slf4j-api</artifactId>
+        <version>${slf4j.version}</version>
+      </dependency>
       <dependency>
         <groupId>org.slf4j</groupId>
         <artifactId>slf4j-log4j12</artifactId>
-        <version>1.7.12</version>
+        <version>${slf4j.version}</version>
       </dependency>
       <dependency>
         <groupId>org.apache.httpcomponents</groupId>
         <artifactId>httpclient</artifactId>
-        <version>4.5.1</version>
+        <version>4.5.2</version>
       </dependency>
       <dependency>
         <groupId>com.netflix.servo</groupId>
         <artifactId>servo-core</artifactId>
-        <version>0.10.0</version> <!-- note: version 0.11.0 is jdk8-only -->
+        <version>0.10.0</version> <!-- note: versions 0.11.0+ (currently 0.12.3) are jdk8-only -->
         <exclusions>
           <exclusion>
             <groupId>com.google.guava</groupId>
@@ -522,7 +543,7 @@
       <dependency>
         <groupId>net.codingwell</groupId>
         <artifactId>scala-guice_2.10</artifactId>
-        <version>4.0.0</version>
+        <version>4.0.1</version>
       </dependency>
     </dependencies>
   </dependencyManagement>