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BinaryCodec.readBytesOrFewer fails if no data is requested AND no date is available in the underlying input stream #1188

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merged 3 commits into from
Oct 5, 2018
Merged

BinaryCodec.readBytesOrFewer fails if no data is requested AND no date is available in the underlying input stream #1188

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cbe2383
Test to show BinaryCodec.readBytesOrFewer will fail if the input stre…
nh13 Oct 5, 2018
6d40e0a
Bug fix: BinaryCodec should not fail when both reading and no bytes a…
nh13 Oct 5, 2018
e3625e7
fixups and developer note
nh13 Oct 5, 2018
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5 changes: 4 additions & 1 deletion src/main/java/htsjdk/samtools/util/BinaryCodec.java
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Original file line number Diff line number Diff line change
Expand Up @@ -415,7 +415,10 @@ public int readBytesOrFewer(final byte[] buffer, final int offset, final int len
throw new IllegalStateException("Calling read method on BinaryCodec open for write.");
}
try {
return inputStream.read(buffer, offset, length);
// Some implementations of InputStream do not behave well when the buffer is empty and length is zero, for
// example ByteArrayInputStream, so we must check for length equal to zero.
// See: https://bugs.java.com/view_bug.do?bug_id=6766844
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good find, thanks for adding this note.

return (length == 0) ? 0 : inputStream.read(buffer, offset, length);
} catch (IOException e) {
throw new RuntimeIOException(constructErrorMessage("Read error"), e);
}
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15 changes: 8 additions & 7 deletions src/test/java/htsjdk/samtools/util/BinaryCodecTest.java
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Expand Up @@ -27,12 +27,7 @@
import org.testng.Assert;
import org.testng.annotations.Test;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.*;


/*
Expand Down Expand Up @@ -284,5 +279,11 @@ public void timeTest() throws IOException{
readCodec.close();
}


@Test
public void testReadBytesOrFewerNoneAvailable() {
final byte[] value = new byte[0];
final ByteArrayInputStream instream = new ByteArrayInputStream(value);
final BinaryCodec readCodec = new BinaryCodec(instream);
Assert.assertEquals(readCodec.readBytesOrFewer(value, 0, 0), 0);
}
}