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Add safety net to BAQ calculation: explicitly cast to byte/int and check for bad values 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4954 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-06 18:09:12 +00:00
parent 2ac5c52281
commit f3ca2cc9de
1 changed files with 14 additions and 4 deletions
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18
java/src/org/broadinstitute/sting/utils/baq/BAQ.java
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@ -6,6 +6,7 @@ import net.sf.samtools.CigarOperator;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.ReferenceSequence;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
/*
The topology of the profile HMM:
@ -369,8 +370,13 @@ public class BAQ {
// At the i-th read base, BAQi = Qi - (BQi - 64) where Qi is the i-th base quality.
// so BQi = Qi - BAQi + 64
byte[] bqTag = new byte[baq.length];
for ( int i = 0; i < bqTag.length; i++)
bqTag[i] = (byte)(((int)read.getBaseQualities()[i] + 64) - baq[i]);
for ( int i = 0; i < bqTag.length; i++) {
int bq = (int)read.getBaseQualities()[i] + 64;
int baq_i = (int)baq[i];
int tag = bq - baq_i;
if ( tag < 0 ) throw new ReviewedStingException("BAQ tag calculation error. BAQ value above base quality at " + read);
bqTag[i] = (byte)tag;
}
return new String(bqTag);
}
@ -406,8 +412,12 @@ public class BAQ {
// At the i-th read base, BAQi = Qi - (BQi - 64) where Qi is the i-th base quality.
newQuals = overwriteOriginalQuals ? rawQuals : new byte[rawQuals.length];
for ( int i = 0; i < rawQuals.length; i++) {
int val = rawQuals[i] - (baq[i] - 64);
newQuals[i] = val < 0 ? 0 : (byte)val;
int rawQual = (int)rawQuals[i];
int baq_delta = (int)baq[i] - 64;
int newval = rawQual - baq_delta;
if ( newval < 0 )
throw new UserException.MalformedBam(read, "BAQ tag error: the BAQ value is larger than the base quality");
newQuals[i] = (byte)newval;
}
} else if ( ! useRawQualsIfNoBAQTag ) {
throw new IllegalStateException("Required BAQ tag to be present, but none was on read " + read.getReadName());