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Merged bug fix from Stable into Unstable

This commit is contained in:
Matt Hanna 2012-01-17 11:08:35 -05:00
parent aa8a885a5b 3ba918aff1
commit 32ccde374b
1 changed files with 7 additions and 7 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
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@ -88,7 +88,7 @@ public class GATKBAMIndex {
seek(0);
final byte[] buffer = readBytes(4);
if (!Arrays.equals(buffer, BAM_INDEX_MAGIC)) {
throw new RuntimeException("Invalid file header in BAM index " + mFile +
throw new ReviewedStingException("Invalid file header in BAM index " + mFile +
": " + new String(buffer));
}
@ -112,7 +112,7 @@ public class GATKBAMIndex {
openIndexFile();
if (referenceSequence >= sequenceCount)
throw new ReviewedStingException("Invalid sequence number " + referenceSequence);
throw new ReviewedStingException("Invalid sequence number " + referenceSequence + " in index file " + mFile);
skipToSequence(referenceSequence);
@ -183,12 +183,12 @@ public class GATKBAMIndex {
public int getLevelForBin(final Bin bin) {
GATKBin gatkBin = new GATKBin(bin);
if(gatkBin.getBinNumber() >= MAX_BINS)
throw new SAMException("Tried to get level for invalid bin.");
throw new ReviewedStingException("Tried to get level for invalid bin in index file " + mFile);
for(int i = getNumIndexLevels()-1; i >= 0; i--) {
if(gatkBin.getBinNumber() >= LEVEL_STARTS[i])
return i;
}
throw new SAMException("Unable to find correct bin for bin "+bin);
throw new ReviewedStingException("Unable to find correct bin for bin " + bin + " in index file " + mFile);
}
/**
@ -352,7 +352,7 @@ public class GATKBAMIndex {
fileChannel.read(buffer);
}
catch(IOException ex) {
throw new ReviewedStingException("Index: unable to read bytes from index file.");
throw new ReviewedStingException("Index: unable to read bytes from index file " + mFile);
}
}
@ -379,7 +379,7 @@ public class GATKBAMIndex {
fileChannel.position(fileChannel.position() + count);
}
catch(IOException ex) {
throw new ReviewedStingException("Index: unable to reposition file channel.");
throw new ReviewedStingException("Index: unable to reposition file channel of index file " + mFile);
}
}
@ -388,7 +388,7 @@ public class GATKBAMIndex {
fileChannel.position(position);
}
catch(IOException ex) {
throw new ReviewedStingException("Index: unable to reposition of file channel.");
throw new ReviewedStingException("Index: unable to reposition of file channel of index file " + mFile);
}
}