Add bz2 support

Author: iychoi

src/libra/common/helpers/PathHelper.java

@@ -21,7 +21,7 @@
  */
 public class PathHelper {
 
-    private static final String[] COMPRESSED_EXT = {"gz"};
+    private static final String[] COMPRESSED_EXT = {"gz", "bz2"};
 
     public static String getParent(String path) {
         // check root
@@ -59,7 +59,7 @@ public static String concatPath(String path1, String path2) {
         return sb.toString();
     }
 
-    public static String getExtensionWithoutCompressed(String name) {
+    public static String getExtensionOfDecompressedFile(String name) {
         String myname = name;
         int idx = myname.lastIndexOf(".");
         if(idx > 0) {

src/libra/common/sequence/FastaPathFilter.java

@@ -29,7 +29,7 @@ public class FastaPathFilter implements PathFilter {
 
     @Override
     public boolean accept(Path path) {
-        String ext = PathHelper.getExtensionWithoutCompressed(path.getName());
+        String ext = PathHelper.getExtensionOfDecompressedFile(path.getName());
         if(ext != null) {
             ext = ext.toLowerCase();
         }

src/libra/common/sequence/FastqPathFilter.java

@@ -29,7 +29,7 @@ public class FastqPathFilter implements PathFilter {
 
     @Override
     public boolean accept(Path path) {
-        String ext = PathHelper.getExtensionWithoutCompressed(path.getName());
+        String ext = PathHelper.getExtensionOfDecompressedFile(path.getName());
         if(ext != null) {
             ext = ext.toLowerCase();
         }