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GATKBAMIndex now passes unit test! Problem was that SeekableBufferedStream seems to have a bug: it will read beyond the end of a file if asked to.

This commit is contained in:
Yossi Farjoun 2012-12-18 17:22:34 -05:00
parent 002ce9c1d5
commit 6ed9eb3da9
1 changed files with 4 additions and 1 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
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@ -359,7 +359,10 @@ public class GATKBAMIndex {
int bytesExpected = buffer.limit();
//BufferedInputStream cannot read directly into a byte buffer, so we read into an array
//and put the result into the bytebuffer after the if statement.
int bytesRead = bufferedStream.read(byteArray,0,bytesExpected);
//SeekableBufferedStream is evil, it will "read" beyond the end of the file if you let it!
final int bytesToRead = (int) Math.min(bufferedStream.length() - bufferedStream.position(), bytesExpected); //min of int and long will definitely be castable to an int.
int bytesRead = bufferedStream.read(byteArray,0,bytesToRead);
// We have a rigid expectation here to read in exactly the number of bytes we've limited
// our buffer to -- if we read in fewer bytes than this, or encounter EOF (-1), the index