Merge 528c3f5 into 9f17a0f

bigdatagenomics · May 19, 2019 · c49ba42 · c49ba42
2 parents 9f17a0f + 528c3f5
commit c49ba42
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Showing 5 changed files with 178 additions and 166 deletions.
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/FlagStat.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/FlagStat.scala
@@ -36,11 +36,11 @@ object FlagStat extends BDGCommandCompanion {
 
 class FlagStatArgs extends Args4jBase {
   @Argument(required = true, metaVar = "INPUT", usage = "The ADAM data to return stats for", index = 0)
-  val inputPath: String = null
+  var inputPath: String = null
   @Args4jOption(required = false, name = "-o", usage = "Optionally write the stats to this file.")
-  val outputPath: String = null
+  var outputPath: String = null
   @Args4jOption(required = false, name = "-stringency", usage = "Set the parsing stringency: SILENT, LENIENT, STRICT.")
-  val stringency: String = "SILENT"
+  var stringency: String = "SILENT"
 }
 
 class FlagStat(protected val args: FlagStatArgs) extends BDGSparkCommand[FlagStatArgs] {

diff --git a/adam-python/Makefile b/adam-python/Makefile
@@ -81,7 +81,8 @@ clean_sdist:
 
 test: check_build_reqs
 	mkdir -p target
-	$(python) -m pytest -vv --junitxml target/pytest-reports/tests.xml $(tests)
+	PYSPARK_SUBMIT_ARGS="--conf spark.executor.memory=4g --conf spark.driver.memory=4g $PYSPARK_SUBMIT_ARGS" \
+		$(python) -m pytest -vv --junitxml target/pytest-reports/tests.xml $(tests)
 
 
 pypi: check_clean_working_copy

diff --git a/adam-python/bdgenomics/adam/test/__init__.py b/adam-python/bdgenomics/adam/test/__init__.py
@@ -57,7 +57,10 @@ def checkFiles(self, file1, file2):
     def setUp(self):
         self._old_sys_path = list(sys.path)
         class_name = self.__class__.__name__
-        self.ss = SparkSession.builder.master('local[4]').appName(class_name).getOrCreate()
+        self.ss = SparkSession.builder \
+                              .master('local[4]') \
+                              .appName(class_name) \
+                              .getOrCreate()
         self.sc = self.ss.sparkContext
 
 

diff --git a/pom.xml b/pom.xml
@@ -588,6 +588,11 @@
         <artifactId>adam-codegen-spark2_${scala.version.prefix}</artifactId>
         <version>${project.version}</version>
       </dependency>
+      <dependency>
+        <groupId>com.thoughtworks.paranamer</groupId>
+        <artifactId>paranamer</artifactId>
+        <version>2.8</version>
+      </dependency>
     </dependencies>
   </dependencyManagement>