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fixing bug in SeekableHttpStream.read #1182

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merged 2 commits into from
Sep 26, 2018
Merged

fixing bug in SeekableHttpStream.read #1182

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c9e2f04
fixing bug in SeekableHttpStream.read
lbergelson Sep 25, 2018
6107b8d
fix formatting
lbergelson Sep 26, 2018
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5 changes: 4 additions & 1 deletion src/main/java/htsjdk/samtools/seekablestream/SeekableHTTPStream.java
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Original file line number Diff line number Diff line change
Expand Up @@ -100,9 +100,12 @@ public int read(byte[] buffer, int offset, int len) throws IOException {
if (offset < 0 || len < 0 || (offset + len) > buffer.length) {
throw new IndexOutOfBoundsException("Offset="+offset+",len="+len+",buflen="+buffer.length);
}
if (len == 0 || position == contentLength) {
if (len == 0 ) {
return 0;
}
if (position == contentLength) {
return -1;
}

HttpURLConnection connection = null;
InputStream is = null;
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14 changes: 14 additions & 0 deletions src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
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Expand Up @@ -69,6 +69,20 @@ public void testRandomRead() throws IOException {
assertEquals(buffer1, buffer2);
}

@Test
public void testReadExactlyOneByteAtEndOfFile() throws IOException {
try (final SeekableStream stream = new SeekableHTTPStream(new URL(BAM_URL_STRING))){
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@pshapiro4broad pshapiro4broad Sep 26, 2018 •
edited
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Almost, still missing the space between the ){. If you select the line and use the IDE's Reformat Code it will fix it for you.

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whoops, didn't see your comment until after I merged

byte[] buff = new byte[1];
long length = stream.length();
stream.seek(length - 1);
Assert.assertFalse(stream.eof());
Assert.assertEquals(stream.read(buff), 1);
Assert.assertTrue(stream.eof());
Assert.assertEquals(stream.read(buff), -1);
}
}


/**
* Test an attempt to read past the end of the file. The test file is 594,149 bytes in length. The test
* attempts to read a 1000 byte block starting at position 594000. A correct result would return 149 bytes.
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