[ADAM-1834] Add proper extensions for SAM/BAM/CRAM output formats.

Resolves #1834.

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)

adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala

@@ -296,7 +296,7 @@ class AlignmentRecordRDDSuite extends ADAMFunSuite {
     ardd.saveAsSam(tempFile.toAbsolutePath.toString + "/reads12.sam",
       asType = Some(SAMFormat.SAM))
 
-    val rdd12B = sc.loadBam(tempFile.toAbsolutePath.toString + "/reads12.sam/part-r-00000")
+    val rdd12B = sc.loadBam(tempFile.toAbsolutePath.toString + "/reads12.sam/part-r-00000.sam")
 
     assert(rdd12B.rdd.count() === rdd12A.rdd.count())
 
@@ -358,7 +358,7 @@ class AlignmentRecordRDDSuite extends ADAMFunSuite {
       asSingleFile = false,
       isSorted = true)
 
-    val rddB = sc.loadBam(tempFile + "/part-r-00000")
+    val rddB = sc.loadBam(tempFile + "/part-r-00000.cram")
 
     assert(rddB.rdd.count() === rddA.rdd.count())
 

adam-core/src/test/scala/org/bdgenomics/adam/util/ParallelFileMergerSuite.scala

@@ -155,7 +155,7 @@ class ParallelFileMergerSuite extends ADAMFunSuite {
 
     val fs = FileSystem.get(sc.hadoopConfiguration)
     val filesToMerge = (Seq(outPath + "_head") ++ (0 until 4).map(i => {
-      outPath + "_tail/part-r-0000%d".format(i)
+      outPath + "_tail/part-r-0000%d.sam".format(i)
     })).map(new Path(_))
       .map(p => (p.toString, 0L, fs.getFileStatus(p).getLen().toLong - 1L))
 
@@ -179,7 +179,7 @@ class ParallelFileMergerSuite extends ADAMFunSuite {
 
     val fs = FileSystem.get(sc.hadoopConfiguration)
     val filesToMerge = (Seq(outPath + "_head") ++ (0 until 4).map(i => {
-      outPath + "_tail/part-r-0000%d".format(i)
+      outPath + "_tail/part-r-0000%d.bam".format(i)
     })).map(new Path(_))
       .map(p => (p.toString, 0L, fs.getFileStatus(p).getLen().toLong - 1L))
 
@@ -206,7 +206,7 @@ class ParallelFileMergerSuite extends ADAMFunSuite {
 
     val fs = FileSystem.get(sc.hadoopConfiguration)
     val filesToMerge = (Seq(outPath + "_head") ++ (0 until 4).map(i => {
-      outPath + "_tail/part-r-0000%d".format(i)
+      outPath + "_tail/part-r-0000%d.cram".format(i)
     })).map(new Path(_))
       .map(p => (p.toString, 0L, fs.getFileStatus(p).getLen().toLong - 1L))