update adam dependency version to 0.30.0

heuermh · Dec 22, 2019 · 4c44924 · 4c44924
1 parent 4268756
commit 4c44924
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Showing 6 changed files with 22 additions and 22 deletions.
diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@ Install
  * Scala 2.11.12 or later, http://www.scala-lang.org
  * Apache Maven 3.3.1 or later, http://maven.apache.org
  * Apache Spark 2.4.4 or later, http://spark.apache.org
- * ADAM: Genomic Data System 0.30.0-SNAPSHOT or later, https://github.com/bigdatagenomics/adam
+ * ADAM: Genomic Data System 0.30.0 or later, https://github.com/bigdatagenomics/adam
 
 
 To build

diff --git a/pom.xml b/pom.xml
@@ -35,7 +35,7 @@
     </developer>
   </developers>
   <properties>
-    <adam.version>0.29.0</adam.version>
+    <adam.version>0.30.0</adam.version>
     <scala.version>2.11.12</scala.version>
     <scala.artifact.suffix>2.11</scala.artifact.suffix>
     <spark.version>2.4.4</spark.version>

diff --git a/src/main/java/com/github/heuermh/adam/commands/JavaCountAlignments.java b/src/main/java/com/github/heuermh/adam/commands/JavaCountAlignments.java
@@ -34,9 +34,9 @@
 
 import org.bdgenomics.adam.rdd.ADAMContext;
 
-import org.bdgenomics.adam.rdd.read.AlignmentRecordDataset;
+import org.bdgenomics.adam.rdd.read.AlignmentDataset;
 
-import org.bdgenomics.formats.avro.AlignmentRecord;
+import org.bdgenomics.formats.avro.Alignment;
 
 import org.bdgenomics.utils.instrumentation.DurationFormatting;
 
@@ -91,12 +91,12 @@ public void run() {
     private void run(final SparkContext sc) {
         ADAMContext ac = new ADAMContext(sc);
         JavaADAMContext javaAdamContext = new JavaADAMContext(ac);
-        AlignmentRecordDataset alignments = javaAdamContext.loadAlignments(inputPath);
-        JavaRDD<AlignmentRecord> jrdd = alignments.jrdd();
+        AlignmentDataset alignments = javaAdamContext.loadAlignments(inputPath);
+        JavaRDD<Alignment> jrdd = alignments.jrdd();
 
-        JavaRDD<String> contigNames = jrdd.map(new Function<AlignmentRecord, String>() {
+        JavaRDD<String> contigNames = jrdd.map(new Function<Alignment, String>() {
                 @Override
-                public String call(final AlignmentRecord rec) {
+                public String call(final Alignment rec) {
                     return rec.getReadMapped() ? rec.getReferenceName() : "unmapped";
                 }
             });

diff --git a/src/main/java/com/github/heuermh/adam/commands/JavaCountAlignmentsPerRead.java b/src/main/java/com/github/heuermh/adam/commands/JavaCountAlignmentsPerRead.java
@@ -34,9 +34,9 @@
 
 import org.bdgenomics.adam.rdd.ADAMContext;
 
-import org.bdgenomics.adam.rdd.read.AlignmentRecordDataset;
+import org.bdgenomics.adam.rdd.read.AlignmentDataset;
 
-import org.bdgenomics.formats.avro.AlignmentRecord;
+import org.bdgenomics.formats.avro.Alignment;
 
 import org.bdgenomics.utils.instrumentation.DurationFormatting;
 
@@ -91,12 +91,12 @@ public void run() {
     private void run(final SparkContext sc) {
         ADAMContext ac = new ADAMContext(sc);
         JavaADAMContext jac = new JavaADAMContext(ac);
-        AlignmentRecordDataset alignments = jac.loadAlignments(inputPath);
-        JavaRDD<AlignmentRecord> jrdd = alignments.jrdd();
+        AlignmentDataset alignments = jac.loadAlignments(inputPath);
+        JavaRDD<Alignment> jrdd = alignments.jrdd();
 
-        JavaRDD<String> contigNames = jrdd.map(new Function<AlignmentRecord, String>() {
+        JavaRDD<String> contigNames = jrdd.map(new Function<Alignment, String>() {
                 @Override
-                public String call(final AlignmentRecord rec) {
+                public String call(final Alignment rec) {
                     return rec.getReadMapped() ? rec.getReadName() : "unmapped";
                 }
             });

diff --git a/src/main/scala/com/github/heuermh/adam/commands/CountAlignments.scala b/src/main/scala/com/github/heuermh/adam/commands/CountAlignments.scala
@@ -20,8 +20,8 @@ import org.apache.spark.SparkContext
 import org.apache.spark.SparkContext._
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.AlignmentRecordDataset
-import org.bdgenomics.formats.avro.AlignmentRecord
+import org.bdgenomics.adam.rdd.read.AlignmentDataset
+import org.bdgenomics.formats.avro.Alignment
 import org.bdgenomics.utils.cli._
 import org.kohsuke.args4j.Argument
 
@@ -48,8 +48,8 @@ class CountAlignments(protected val args: CountAlignmentsArgs) extends BDGSparkC
   val companion = CountAlignments
 
   def run(sc: SparkContext) {
-    var alignments: AlignmentRecordDataset = sc.loadAlignments(args.inputPath)
-    var rdd: RDD[AlignmentRecord] = alignments.rdd
+    var alignments: AlignmentDataset = sc.loadAlignments(args.inputPath)
+    var rdd: RDD[Alignment] = alignments.rdd
 
     rdd.map(rec => if (rec.getReadMapped) rec.getReferenceName else "unmapped")
       .map(referenceName => (referenceName, 1))

diff --git a/src/main/scala/com/github/heuermh/adam/commands/CountAlignmentsPerRead.scala b/src/main/scala/com/github/heuermh/adam/commands/CountAlignmentsPerRead.scala
@@ -20,8 +20,8 @@ import org.apache.spark.SparkContext
 import org.apache.spark.SparkContext._
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.AlignmentRecordDataset
-import org.bdgenomics.formats.avro.AlignmentRecord
+import org.bdgenomics.adam.rdd.read.AlignmentDataset
+import org.bdgenomics.formats.avro.Alignment
 import org.bdgenomics.utils.cli._
 import org.kohsuke.args4j.Argument
 
@@ -48,8 +48,8 @@ class CountAlignmentsPerRead(protected val args: CountAlignmentsPerReadArgs) ext
   val companion = CountAlignmentsPerRead
 
   def run(sc: SparkContext) {
-    var alignments: AlignmentRecordDataset = sc.loadAlignments(args.inputPath)
-    var rdd: RDD[AlignmentRecord] = alignments.rdd
+    var alignments: AlignmentDataset = sc.loadAlignments(args.inputPath)
+    var rdd: RDD[Alignment] = alignments.rdd
 
     rdd.map(rec => if (rec.getReadMapped) rec.getReadName else "unmapped")
       .map(readName => (readName, 1))