From a8b1dea9b50a18ee8086eacb490a85038ee53f69 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 13 May 2011 15:25:54 +0000
Subject: [PATCH] additional constructors to handle files over http and ftp
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16128 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/TabixReader.java | 14 ++++++++++++++
1 file changed, 14 insertions(+)
diff --git a/uk/ac/sanger/artemis/components/variant/TabixReader.java b/uk/ac/sanger/artemis/components/variant/TabixReader.java
index e546ef377..f24380233 100644
--- a/uk/ac/sanger/artemis/components/variant/TabixReader.java
+++ b/uk/ac/sanger/artemis/components/variant/TabixReader.java
@@ -28,8 +28,10 @@ package uk.ac.sanger.artemis.components.variant;
/* Contact: Heng Li <hengli@broadinstitute.org> */
import net.sf.samtools.util.BlockCompressedInputStream;
+import net.sf.samtools.util.SeekableStream;
import java.io.*;
+import java.net.URL;
import java.nio.*;
import java.util.HashMap;
import java.util.ArrayList;
@@ -92,6 +94,18 @@ public class TabixReader extends AbstractVCFReader
mFp = new BlockCompressedInputStream(new File(fn));
readIndex();
}
+
+ public TabixReader(final String fn, final SeekableStream ins) throws IOException {
+ mFn = fn;
+ mFp = new BlockCompressedInputStream(ins);
+ readIndex();
+ }
+
+ public TabixReader(final String fn, final URL url) throws IOException {
+ mFn = fn;
+ mFp = new BlockCompressedInputStream(url);
+ readIndex();
+ }
private static int reg2bins(final int beg, final int _end, final int[] list) {
int i = 0, k, end = _end;
--
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