added check for.bam.bai and .bai index files

bigdatagenomics · Dec 24, 2017 · ee06eda · ee06eda
1 parent bbc4782
commit ee06eda
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Showing 3 changed files with 10 additions and 2 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
@@ -1567,7 +1567,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     // Otherwise, pathName is a directory and the entire path must be searched
     // for indices.
     val indexPath = if (pathName.endsWith(".bam")) {
-      new Path(pathName + ".bai")
+      new Path(pathName.toString.replace(".bam", "*.bai"))
     } else {
       path
     }
@@ -1581,8 +1581,9 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     require(bamFiles.nonEmpty,
       "Did not find any BAM files at %s.".format(path))
 
+    // look for index files named <pathname>.bam.bai and <pathname>.bai
     val missingIndices = bamFiles.filterNot(f => {
-      indexFiles.contains(f.toString + ".bai")
+      indexFiles.contains(f.toString + ".bai") || indexFiles.contains(f.toString.dropRight(3) + "bai")
     })
 
     if (!missingIndices.isEmpty) {

diff --git a/...t/resources/indexed_bams/sorted.2.bam.bai → .../test/resources/indexed_bams/sorted.2.bai b/...t/resources/indexed_bams/sorted.2.bam.bai → .../test/resources/indexed_bams/sorted.2.bai
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala
@@ -443,6 +443,13 @@ class ADAMContextSuite extends ADAMFunSuite {
     }
   }
 
+  sparkTest("loadIndexedBam should work with indexed file with index naming format <filename>.bai") {
+    val refRegion = ReferenceRegion("1", 1, 100)
+    val path = testFile("indexed_bams/sorted.2.bam")
+    val reads = sc.loadIndexedBam(path, refRegion)
+    assert(reads.rdd.count == 1)
+  }
+
   sparkTest("loadIndexedBam glob should throw exception without an index file") {
     val refRegion = ReferenceRegion("1", 26472780, 26472790)
     val path = new File(testFile("bams/small.bam")).getParent()