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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-03-05 17:54:59 -05:00
parent c6ded4d23c e9ad382e74
commit b37461587d
1 changed files with 65 additions and 2 deletions
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67
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
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@ -25,8 +25,14 @@
package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.walkers.recalibration.CountCovariatesGatherer;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/**
* Created by IntelliJ IDEA.
@ -39,6 +45,63 @@ import org.broadinstitute.sting.commandline.Hidden;
public class RecalibrationArgumentCollection {
/**
* This algorithm treats every reference mismatch as an indication of error. However, real genetic variation is expected to mismatch the reference,
* so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites. This tool accepts any number of RodBindings (VCF, Bed, etc.)
* for use as this database. For users wishing to exclude an interval list of known variation simply use -XL my.interval.list to skip over processing those sites.
* Please note however that the statistics reported by the tool will not accurately reflected those sites skipped by the -XL argument.
*/
@Input(fullName = "knownSites", shortName = "knownSites", doc = "A database of known polymorphic sites to skip over in the recalibration algorithm", required = false)
protected List<RodBinding<Feature>> knownSites = Collections.emptyList();
/**
* After the header, data records occur one per line until the end of the file. The first several items on a line are the
* values of the individual covariates and will change depending on which covariates were specified at runtime. The last
* three items are the data- that is, number of observations for this combination of covariates, number of reference mismatches,
* and the raw empirical quality score calculated by phred-scaling the mismatch rate.
*/
@Gather(CountCovariatesGatherer.class)
@Output
protected PrintStream RECAL_FILE;
/**
* List all implemented covariates.
*/
@Argument(fullName = "list", shortName = "ls", doc = "List the available covariates and exit", required = false)
protected boolean LIST_ONLY = false;
/**
* Covariates to be used in the recalibration. Each covariate is given as a separate cov parameter. ReadGroup and ReportedQuality are required covariates and are already added for you. See the list of covariates with -list.
*/
@Argument(fullName = "covariate", shortName = "cov", doc = "Covariates to be used in the recalibration. Each covariate is given as a separate cov parameter. ReadGroup and ReportedQuality are required covariates and are already added for you.", required = false)
protected String[] COVARIATES = null;
/*
* Use the standard set of covariates in addition to the ones listed using the -cov argument
*/
@Argument(fullName = "standard_covs", shortName = "standard", doc = "Use the standard set of covariates in addition to the ones listed using the -cov argument", required = false)
protected boolean USE_STANDARD_COVARIATES = true;
/////////////////////////////
// Debugging-only Arguments
/////////////////////////////
/**
* This calculation is critically dependent on being able to skip over known polymorphic sites. Please be sure that you know what you are doing if you use this option.
*/
@Hidden
@Argument(fullName = "run_without_dbsnp_potentially_ruining_quality", shortName = "run_without_dbsnp_potentially_ruining_quality", required = false, doc = "If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only.")
protected boolean RUN_WITHOUT_DBSNP = false;
/////////////////////////////
// protected Member Variables
/////////////////////////////
protected final RecalDataManager dataManager = new RecalDataManager(); // Holds the data HashMap used to create collapsed data hashmaps (delta delta tables)
protected final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>();// A list to hold the covariate objects that were requested
protected final String SKIP_RECORD_ATTRIBUTE = "SKIP"; // used to label reads that should be skipped.
protected final String SEEN_ATTRIBUTE = "SEEN"; // used to label reads as processed.
/**
* CountCovariates and TableRecalibration accept a --solid_recal_mode <MODE> flag which governs how the recalibrator handles the
* reads which have had the reference inserted because of color space inconsistencies.