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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-09-30 15:51:09 -04:00
parent a881d6f145 05fba6f23a
commit 010899f886
2 changed files with 15 additions and 4 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -170,9 +170,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
/////////////////////////////
private RecalDataManager dataManager; // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // List of covariates to be used in this calculation
private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
public static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
public static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
public static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
public static final String EOF_MARKER = "EOF";
private long numReadsWithMalformedColorSpace = 0;

13
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -888,9 +888,20 @@ public class ReadUtils {
if (endsWithinCigar)
fallsInsideDeletion = cigarElement.getOperator() == CigarOperator.DELETION;
// if we end outside the current cigar element, we need to check if the next element is a deletion.
// if we end outside the current cigar element, we need to check if the next element is an insertion or deletion.
else {
nextCigarElement = cigarElementIterator.next();
// if it's an insertion, we need to clip the whole insertion before looking at the next element
if (nextCigarElement.getOperator() == CigarOperator.INSERTION) {
readBases += nextCigarElement.getLength();
if (!cigarElementIterator.hasNext())
throw new ReviewedStingException("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- call Mauricio");
nextCigarElement = cigarElementIterator.next();
}
// if it's a deletion, we will pass the information on to be handled downstream.
fallsInsideDeletion = nextCigarElement.getOperator() == CigarOperator.DELETION;
}