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Few category changes

This commit is contained in:
Mauricio Carneiro 2012-07-25 17:23:02 -04:00
parent 05fa377a8e
commit fce5cb9f35
2 changed files with 4 additions and 8 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -44,16 +44,15 @@ import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*; import java.util.*;
/** /**
* All command line parameters accepted by all tools in the GATK.
*
* The GATK engine itself. Manages map/reduce data access and runs walkers. * The GATK engine itself. Manages map/reduce data access and runs walkers.
* *
* We run command line GATK programs using this class. It gets the command line args, parses them, and hands the * We run command line GATK programs using this class. It gets the command line args, parses them, and hands the
* gatk all the parsed out information. Pretty much anything dealing with the underlying system should go here, * gatk all the parsed out information. Pretty much anything dealing with the underlying system should go here,
* the gatk engine should deal with any data related information. * the gatk engine should deal with any data related information.
*/ */
@DocumentedGATKFeature( @DocumentedGATKFeature(groupName = "GATK Engine")
groupName = "GATK Engine",
summary = "Features and arguments for the GATK engine itself, available to all walkers.",
extraDocs = { UserException.class })
public class CommandLineGATK extends CommandLineExecutable { public class CommandLineGATK extends CommandLineExecutable {
@Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run") @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
private String analysisName = null; private String analysisName = null;

5
public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
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@ -49,10 +49,7 @@ import java.util.List;
@ReadFilters(MalformedReadFilter.class) @ReadFilters(MalformedReadFilter.class)
@PartitionBy(PartitionType.NONE) @PartitionBy(PartitionType.NONE)
@BAQMode(QualityMode = BAQ.QualityMode.OVERWRITE_QUALS, ApplicationTime = BAQ.ApplicationTime.ON_INPUT) @BAQMode(QualityMode = BAQ.QualityMode.OVERWRITE_QUALS, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
@DocumentedGATKFeature( @DocumentedGATKFeature(groupName = "Uncategorized", extraDocs = {CommandLineGATK.class})
groupName = "GATK walkers",
summary = "General tools available for running on the command line as part of the GATK package",
extraDocs = {CommandLineGATK.class})
public abstract class Walker<MapType, ReduceType> { public abstract class Walker<MapType, ReduceType> {
final protected static Logger logger = Logger.getLogger(Walker.class); final protected static Logger logger = Logger.getLogger(Walker.class);
private GenomeAnalysisEngine toolkit; private GenomeAnalysisEngine toolkit;