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Fixing up some comments in the BQSR

This commit is contained in:
Ryan Poplin 2011-08-11 08:36:00 -04:00
parent f1b09db39e
commit dd5fe8291d
2 changed files with 7 additions and 8 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
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@ -100,7 +100,7 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
///////////////////////////// /////////////////////////////
// Command Line Arguments // Command Line Arguments
///////////////////////////// /////////////////////////////
@Output(fullName="recal_file", shortName="recalFile", required=true, doc="Filename for the outputted covariates table recalibration file") @Output(fullName="recal_file", shortName="recalFile", required=true, doc="Filename for the output covariates table recalibration file")
@Gather(CountCovariatesGatherer.class) @Gather(CountCovariatesGatherer.class)
public PrintStream RECAL_FILE; public PrintStream RECAL_FILE;
@ -124,8 +124,8 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
///////////////////////////// /////////////////////////////
private final RecalDataManager dataManager = new RecalDataManager(); // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps private final RecalDataManager dataManager = new RecalDataManager(); // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // A list to hold the covariate objects that were requested private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // A list to hold the covariate objects that were requested
private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0; // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878) private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0; // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878)
private static int DBSNP_VALIDATION_CHECK_FREQUENCY = 1000000; // how often to validate dbsnp mismatch rate (in terms of loci seen) private static int DBSNP_VALIDATION_CHECK_FREQUENCY = 1000000; // how often to validate dbsnp mismatch rate (in terms of loci seen)
public static class CountedData { public static class CountedData {
private long countedSites = 0; // Number of loci used in the calculations, used for reporting in the output file private long countedSites = 0; // Number of loci used in the calculations, used for reporting in the output file
@ -136,7 +136,7 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
private long dbSNPCountsMM = 0, dbSNPCountsBases = 0; // mismatch/base counts for dbSNP loci private long dbSNPCountsMM = 0, dbSNPCountsBases = 0; // mismatch/base counts for dbSNP loci
private long novelCountsMM = 0, novelCountsBases = 0; // mismatch/base counts for non-dbSNP loci private long novelCountsMM = 0, novelCountsBases = 0; // mismatch/base counts for non-dbSNP loci
private int lociSinceLastDbsnpCheck = 0; // loci since last dbsnp validation private int lociSinceLastDbsnpCheck = 0; // loci since last dbsnp validation
/** /**
* Adds the values of other to this, returning this * Adds the values of other to this, returning this
@ -298,8 +298,8 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
CountedData counter = new CountedData(); CountedData counter = new CountedData();
if( !isSNP ) { if( !isSNP ) {
// For each read at this locus // For each read at this locus
for( PileupElement p : context.getBasePileup() ) { for( final PileupElement p : context.getBasePileup() ) {
GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead(); final GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
int offset = p.getOffset(); int offset = p.getOffset();
if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE ) ) { if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE ) ) {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -93,8 +93,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
@Output(doc="The output BAM file", required=true) @Output(doc="The output BAM file", required=true)
private StingSAMFileWriter OUTPUT_BAM = null; private StingSAMFileWriter OUTPUT_BAM = null;
@Argument(fullName="preserve_qscores_less_than", shortName="pQ", @Argument(fullName="preserve_qscores_less_than", shortName="pQ", doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
private int PRESERVE_QSCORES_LESS_THAN = 5; private int PRESERVE_QSCORES_LESS_THAN = 5;
@Argument(fullName="smoothing", shortName="sm", required = false, doc="Number of imaginary counts to add to each bin in order to smooth out bins with few data points, default=1") @Argument(fullName="smoothing", shortName="sm", required = false, doc="Number of imaginary counts to add to each bin in order to smooth out bins with few data points, default=1")
private int SMOOTHING = 1; private int SMOOTHING = 1;