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Adding ability to read in and make use of kmer quality tables during HMM evaluation

This commit is contained in:
Ryan Poplin 2011-09-29 07:46:19 -04:00
parent 9e32ede5b2
commit e366ee18bc
1 changed files with 3 additions and 3 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 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 final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // List of covariates to be used in this calculation
private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*"); public static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*"); public static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*"); public static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
public static final String EOF_MARKER = "EOF"; public static final String EOF_MARKER = "EOF";
private long numReadsWithMalformedColorSpace = 0; private long numReadsWithMalformedColorSpace = 0;