JAL-2909 Read in a bam file - but strand/location unaware

[jalview.git] / src / jalview / io / FileFormat.java

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 4b33dbf..21fadd2 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -347,6 +347,27 @@ public enum FileFormat implements FileFormatI
       return true;
     }
   },
+  Bam("bam", "bam", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new BamFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new BamFile();
+    }
+
+    @Override
+    public boolean isStructureFile()
+    {
+      return false;
+    }
+  },
   Jalview("Jalview", "jar,jvp", true, true)
   {
     @Override