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Merge pull request #9 from yfarjoun/speedy 

GATKBAMIndex now passes unit test!
This commit is contained in:
eitanbanks 2012-12-18 15:31:11 -08:00
parent 002ce9c1d5 6ed9eb3da9
commit c86f5e46b0
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(); int bytesExpected = buffer.limit();
//BufferedInputStream cannot read directly into a byte buffer, so we read into an array //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. //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 // 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 // our buffer to -- if we read in fewer bytes than this, or encounter EOF (-1), the index