Merge 797fe02 into d213820

Author: fnothaft

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

@@ -47,7 +47,7 @@ class ADAMBAMOutputFormat[K]
     readSAMHeaderFrom(path, conf)
 
     // now that we have the header set, we need to make a record reader
-    return new KeyIgnoringBAMRecordWriter[K](getDefaultWorkFile(context, ""),
+    return new KeyIgnoringBAMRecordWriter[K](getDefaultWorkFile(context, ".bam"),
       header,
       true,
       context)
@@ -84,7 +84,7 @@ class ADAMBAMOutputFormatHeaderLess[K]
     readSAMHeaderFrom(path, conf)
 
     // now that we have the header set, we need to make a record reader
-    return new KeyIgnoringBAMRecordWriter[K](getDefaultWorkFile(context, ""),
+    return new KeyIgnoringBAMRecordWriter[K](getDefaultWorkFile(context, ".bam"),
       header,
       false,
       context)

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

@@ -47,7 +47,7 @@ class ADAMCRAMOutputFormat[K]
     readSAMHeaderFrom(path, conf)
 
     // now that we have the header set, we need to make a record reader
-    return new KeyIgnoringCRAMRecordWriter[K](getDefaultWorkFile(context, ""),
+    return new KeyIgnoringCRAMRecordWriter[K](getDefaultWorkFile(context, ".cram"),
       header,
       true,
       context)
@@ -84,7 +84,7 @@ class ADAMCRAMOutputFormatHeaderLess[K]
     readSAMHeaderFrom(path, conf)
 
     // now that we have the header set, we need to make a record reader
-    return new KeyIgnoringCRAMRecordWriter[K](getDefaultWorkFile(context, ""),
+    return new KeyIgnoringCRAMRecordWriter[K](getDefaultWorkFile(context, ".cram"),
       header,
       false,
       context)

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

@@ -44,7 +44,7 @@ class ADAMSAMOutputFormat[K]
     readSAMHeaderFrom(path, conf)
 
     // now that we have the header set, we need to make a record reader
-    return new KeyIgnoringSAMRecordWriter(getDefaultWorkFile(context, ""),
+    return new KeyIgnoringSAMRecordWriter(getDefaultWorkFile(context, ".sam"),
       header,
       true,
       context)
@@ -71,7 +71,7 @@ class ADAMSAMOutputFormatHeaderLess[K]
     readSAMHeaderFrom(path, conf)
 
     // now that we have the header set, we need to make a record reader
-    return new KeyIgnoringSAMRecordWriter(getDefaultWorkFile(context, ""),
+    return new KeyIgnoringSAMRecordWriter(getDefaultWorkFile(context, ".sam"),
       header,
       false,
       context)