clean up

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

@@ -180,18 +180,6 @@ object ReferenceRegion {
     }
   }
 
-  /**
-   * Builds a referenceRegion from genomic coordinates.
-   *
-   * @param referenceName reference name
-   * @param start start position
-   * @param end end position
-   * @return Reference Region for these genomic coordinates
-   */
-  def fromGenomicRange(referenceName: String, start: Long, end: Long): ReferenceRegion = {
-    ReferenceRegion(referenceName, start, end)
-  }
-
   /**
    * Builds a reference region for a called genotype.
    *
@@ -214,6 +202,18 @@ object ReferenceRegion {
     ReferenceRegion(variant.getContigName, variant.getStart, variant.getEnd)
   }
 
+  /**
+   * Builds a referenceRegion from genomic coordinates.
+   *
+   * @param referenceName reference name
+   * @param start start position
+   * @param end end position
+   * @return Reference Region for these genomic coordinates
+   */
+  def fromGenomicRange(referenceName: String, start: Long, end: Long): ReferenceRegion = {
+    ReferenceRegion(referenceName, start, end)
+  }
+
   private def checkRead(record: AlignmentRecord) {
     require(record.getReadMapped,
       "Cannot build reference region for unmapped read %s.".format(record))

adam-python/bdgenomics/adam/models.py

@@ -18,7 +18,7 @@
 
 class ReferenceRegion():
 
-    def __init__(self, chr, start, end):
+    def __init__(self, referenceName, start, end):
         """
         Represents a contiguous region of the reference genome.
 
@@ -29,7 +29,7 @@ def __init__(self, chr, start, end):
         half-open interval.
         """
 
-        self.chr = chr
+        self.referenceName = referenceName
         self.start = start
         self.end = end
 
@@ -43,4 +43,4 @@ def _toJava(self, jvm):
         :param jvm: Py4j JVM handle.
         """
 
-        return jvm.org.bdgenomics.adam.models.ReferenceRegion.fromGenomicRange(self.chr, self.start, self.end)
+        return jvm.org.bdgenomics.adam.models.ReferenceRegion.fromGenomicRange(self.referenceName, self.start, self.end)

adam-python/bdgenomics/adam/rdd.py

@@ -19,7 +19,6 @@
 import logging
 
 from py4j.java_gateway import get_java_class
-from py4j.java_collections import JavaIterator
 from pyspark.rdd import RDD
 from pyspark.sql import DataFrame, SQLContext
 
@@ -94,10 +93,7 @@ def filterByOverlappingRegions(self, querys):
 
         # translate reference regions into iterator of jvm types
         javaRrs = iter([q._toJava(self.sc._jvm) for q in querys])
-	print("!!!!!!!!!!!!!!!!JAVA RRs!!!!!!!!!!!!!!")
-	print(javaRrs)
-        print(type(javaRrs))
-
+
         return self._replaceRdd(self._jvmRdd.filterByOverlappingRegions(javaRrs))
 
     def union(self, rdds):

adam-python/bdgenomics/adam/test/coverageRdd_test.py

@@ -35,8 +35,7 @@ def test_save(self):
         coverage.save(tmpPath,
                               asSingleFile=True,
                             disableFastConcat=True)
-	print(os.listdir(tmpPath))
-	assert(os.listdir(tmpPath) != []) 
+    	assert(os.listdir(tmpPath) != [])
 
 
     def test_collapse(self):

scripts/jenkins-test

@@ -88,6 +88,12 @@ then
     exit 1
 fi
 
+# if those pass, build the distribution package and the integration tests
+mvn -U \
+    test \
+    -P coverage,coveralls  scoverage:report coveralls:report \
+    -DrepoToken=${COVERALLS_REPO_TOKEN} ${COVERALLS_PRB_OPTION}
+
 # make verbose again
 set -x -v