From 752928df941e73da473855b1fe9eda13629b3727 Mon Sep 17 00:00:00 2001 From: hanna Date: Thu, 7 May 2009 01:22:01 +0000 Subject: [PATCH] Switch to better mechanism for supplying a default. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@615 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/GenomeAnalysisTK.java | 1 + .../gatk/walkers/DepthOfCoverageWalker.java | 4 ++-- .../sting/gatk/walkers/PileupWalker.java | 8 ++++---- .../gatk/walkers/ValidatingPileupWalker.java | 4 ++-- .../gatk/walkers/AlleleFrequencyWalker.java | 4 ++-- .../gatk/walkers/CovariateCounterWalker.java | 16 ++++++++-------- .../gatk/walkers/DuplicateQualsWalker.java | 12 ++++++------ .../FindNonrandomSecondBestBasePiles.java | 4 ++-- .../gatk/walkers/HybSelPerformanceWalker.java | 4 ++-- .../gatk/walkers/IOCrusherWalker.java | 8 ++++---- .../gatk/walkers/IndelInspector.java | 8 ++++---- .../gatk/walkers/IndelIntervalWalker.java | 8 ++++---- .../gatk/walkers/IntervalCleanerWalker.java | 4 ++-- .../walkers/LogisticRecalibrationWalker.java | 4 ++-- .../gatk/walkers/Pilot3CoverageWalker.java | 6 +++--- .../playground/gatk/walkers/PoolCaller.java | 2 +- .../gatk/walkers/PoolCallingExperiment.java | 8 ++++---- .../gatk/walkers/ReadErrorRateWalker.java | 6 +++--- .../gatk/walkers/SingleSampleGenotyper.java | 18 +++++++++--------- .../gatk/walkers/SomaticCoverageWalker.java | 4 ++-- .../sting/utils/cmdLine/Argument.java | 6 ------ 21 files changed, 67 insertions(+), 72 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java index 1d373c623..65b41a82c 100644 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java @@ -218,6 +218,7 @@ public class GenomeAnalysisTK extends CommandLineProgram { Walker my_walker = null; try { my_walker = walkerManager.createWalkerByName( Analysis_Name ); + loadArgumentsIntoObject( my_walker ); } catch( InstantiationException ex ) { throw new RuntimeException( "Unable to instantiate walker.", ex ); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java index a8b9cbbe5..cf5ba61c5 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java @@ -15,8 +15,8 @@ import java.util.List; * To change this template use File | Settings | File Templates. */ public class DepthOfCoverageWalker extends LocusWalker> { - @Argument(fullName="suppressLocusPrinting",doc="Suppress printing",required=false,defaultValue="false") - public boolean suppressPrinting; + @Argument(fullName="suppressLocusPrinting",doc="Suppress printing",required=false) + public boolean suppressPrinting = false; public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { if ( !suppressPrinting ) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index fd9db68b4..3d9b00e56 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -15,11 +15,11 @@ import org.broadinstitute.sting.utils.ReadBackedPileup; * To change this template use File | Settings | File Templates. */ public class PileupWalker extends LocusWalker implements TreeReducible { - @Argument(fullName="verbose",doc="verbose",required=false,defaultValue="false") - public boolean VERBOSE; + @Argument(fullName="verbose",doc="verbose",required=false) + public boolean VERBOSE = false; - @Argument(fullName="extended",shortName="ext",doc="extended",required=false,defaultValue="false") - public boolean EXTENDED; + @Argument(fullName="extended",shortName="ext",doc="extended",required=false) + public boolean EXTENDED = false; public boolean FLAG_UNCOVERED_BASES = true; // todo: how do I make this a command line argument? diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java index 9b4e5fbe1..4e1f20a81 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java @@ -17,8 +17,8 @@ import org.broadinstitute.sting.utils.ReadBackedPileup; * To change this template use File | Settings | File Templates. */ public class ValidatingPileupWalker extends LocusWalker { - @Argument(fullName="continue_after_error",doc="Continue after an error",required=false,defaultValue="false") - public boolean CONTINUE_AFTER_AN_ERROR; + @Argument(fullName="continue_after_error",doc="Continue after an error",required=false) + public boolean CONTINUE_AFTER_AN_ERROR = false; public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { Pileup pileup = new ReadBackedPileup(ref, context); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java index b1fe87fc8..5d9077fba 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java @@ -21,10 +21,10 @@ import java.io.DataInputStream; public class AlleleFrequencyWalker extends LocusWalker// implements AllelicVariant { @Argument(doc="Number of chromosomes in data") public int N; - @Argument(required=false,doc="downsample",defaultValue="0") public int DOWNSAMPLE; + @Argument(required=false,doc="downsample") public int DOWNSAMPLE = 0; @Argument(doc="File to output GFF formatted allele frequency calls") public String GFF_OUTPUT_FILE; @Argument(shortName="met", doc="Turns on logging of metrics on the fly with AlleleFrequency calculation") public boolean LOG_METRICS; - @Argument(required=false, defaultValue="metrics.out", doc="Name of file where metrics will output") public String METRICS_OUTPUT_FILE; + @Argument(required=false, doc="Name of file where metrics will output") public String METRICS_OUTPUT_FILE = "metrics.out"; @Argument(required=false, doc="Ignores 4-base probabilities and only uses the quality of the best/called base") public boolean FORCE_1BASE_PROBS; protected static Logger logger = Logger.getLogger(AlleleFrequencyWalker.class); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java index c74db3a50..8d34db30a 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java @@ -15,17 +15,17 @@ import java.io.FileNotFoundException; @WalkerName("CountCovariates") public class CovariateCounterWalker extends LocusWalker { - @Argument(fullName="MAX_READ_LENGTH", shortName="mrl", doc="max read length", required=false,defaultValue="101") - public int MAX_READ_LENGTH; + @Argument(fullName="MAX_READ_LENGTH", shortName="mrl", doc="max read length", required=false) + public int MAX_READ_LENGTH = 101; - @Argument(fullName="MAX_QUAL_SCORE", shortName="mqs", doc="max quality score", required=false,defaultValue="63") - public int MAX_QUAL_SCORE; + @Argument(fullName="MAX_QUAL_SCORE", shortName="mqs", doc="max quality score", required=false) + public int MAX_QUAL_SCORE = 63; - @Argument(fullName="OUTPUT_FILEROOT", shortName="outroot", required=false, defaultValue="output", doc="Filename root for the outputted logistic regression training files") - public String OUTPUT_FILEROOT; + @Argument(fullName="OUTPUT_FILEROOT", shortName="outroot", required=false, doc="Filename root for the outputted logistic regression training files") + public String OUTPUT_FILEROOT = "output"; - @Argument(fullName="CREATE_TRAINING_DATA", shortName="trainingdata", required=false, defaultValue="false", doc="Create training data files for logistic regression") - public boolean CREATE_TRAINING_DATA; + @Argument(fullName="CREATE_TRAINING_DATA", shortName="trainingdata", required=false, doc="Create training data files for logistic regression") + public boolean CREATE_TRAINING_DATA = false; int NDINUCS = 16; RecalData[][][] data = new RecalData[MAX_READ_LENGTH+1][MAX_QUAL_SCORE+1][NDINUCS]; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/DuplicateQualsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/DuplicateQualsWalker.java index ad9bac07d..e7b5672b7 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/DuplicateQualsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/DuplicateQualsWalker.java @@ -109,14 +109,14 @@ class DuplicateComp { * To change this template use File | Settings | File Templates. */ public class DuplicateQualsWalker extends DuplicateWalker, QualityTracker> { - @Argument(fullName="filterUnobservedQuals", shortName="filterUnobservedQuals", required=false, defaultValue="false", doc="Show only quality bins with at least one observation in the data") - public boolean FILTER_UNOBSERVED_QUALS; + @Argument(fullName="filterUnobservedQuals", shortName="filterUnobservedQuals", required=false, doc="Show only quality bins with at least one observation in the data") + public boolean FILTER_UNOBSERVED_QUALS = false; - @Argument(fullName="maxPairwiseCompsPerDupSet", shortName="maxPairwiseCompsPerDupSet", required=false, defaultValue="100", doc="Maximumize number of pairwise comparisons to perform among duplicate read sets") - public int MAX_PAIRSIZE_COMPS_PER_DUPLICATE_SET; + @Argument(fullName="maxPairwiseCompsPerDupSet", shortName="maxPairwiseCompsPerDupSet", required=false, doc="Maximumize number of pairwise comparisons to perform among duplicate read sets") + public int MAX_PAIRSIZE_COMPS_PER_DUPLICATE_SET = 100; - @Argument(fullName="combinedQuals", shortName="combinedQuals", required=false, defaultValue="false", doc="Combine and assess pairwise base qualities") - public boolean COMBINE_QUALS; + @Argument(fullName="combinedQuals", shortName="combinedQuals", required=false, doc="Combine and assess pairwise base qualities") + public boolean COMBINE_QUALS = false; final boolean DEBUG = false; final private boolean ACTUALLY_DO_WORK = true; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/FindNonrandomSecondBestBasePiles.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/FindNonrandomSecondBestBasePiles.java index 8f524b86d..cd1751e6b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/FindNonrandomSecondBestBasePiles.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/FindNonrandomSecondBestBasePiles.java @@ -21,8 +21,8 @@ import java.util.List; import java.util.ArrayList; public class FindNonrandomSecondBestBasePiles extends LocusWalker { - @Argument(fullName="verbose",doc="verbose",required=false,defaultValue="false") - public boolean VERBOSE; + @Argument(fullName="verbose",doc="verbose",required=false) + public boolean VERBOSE = false; private AlleleFrequencyWalker caller_1b; private AlleleFrequencyWalker caller_4b; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java index 021247832..b0fe8a278 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java @@ -12,8 +12,8 @@ import java.util.List; import net.sf.samtools.SAMRecord; public class HybSelPerformanceWalker extends LocusWalker { - @Argument(fullName="min_mapq", shortName="mmq", required=false, defaultValue="1", doc="Minimum mapping quality of reads to consider") public Integer MIN_MAPQ; - @Argument(fullName="include_duplicates", shortName="idup", required=false, defaultValue="false", doc="consider duplicate reads") public Boolean INCLUDE_DUPLICATE_READS; + @Argument(fullName="min_mapq", shortName="mmq", required=false, doc="Minimum mapping quality of reads to consider") public Integer MIN_MAPQ = 1; + @Argument(fullName="include_duplicates", shortName="idup", required=false, doc="consider duplicate reads") public Boolean INCLUDE_DUPLICATE_READS = false; public static class TargetInfo { public int counts = 0; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java index f9d71141b..bae99b408 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java @@ -24,11 +24,11 @@ import java.io.File; * @author Kiran Garimella */ public class IOCrusherWalker extends ReadWalker> { - @Argument(shortName="nWaysOut",doc="n ways out",required=false,defaultValue="1") - public int nWaysOut; + @Argument(shortName="nWaysOut",doc="n ways out",required=false) + public int nWaysOut = 1; - @Argument(shortName="readScaling",doc="read scaling",required=false,defaultValue="1") - public float readScaling; + @Argument(shortName="readScaling",doc="read scaling",required=false) + public float readScaling = 1; @Argument(shortName="outputBase",doc="output base",required=true) public String outputBase; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java index 48d1f9ddb..53cea0268 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java @@ -17,13 +17,13 @@ import edu.mit.broad.picard.reference.ReferenceSequence; @WalkerName("InspectIndels") public class IndelInspector extends ReadWalker { - @Argument(fullName="IndelVerbosity", shortName="iverb", required=false, defaultValue="SILENT", doc="Verbosity level: SILENT, PILESUMMARY, ALIGNMENTS") public String VERBOSITY_LEVEL; + @Argument(fullName="IndelVerbosity", shortName="iverb", required=false, doc="Verbosity level: SILENT, PILESUMMARY, ALIGNMENTS") public String VERBOSITY_LEVEL = "SILENT"; @Argument(fullName="OutputNormal", shortName="outNorm", required=true, doc="Output file (sam or bam) for non-indel related reads and indel reads that were not improved") public String OUT1; @Argument(fullName="OutputIndel", shortName="outIndel", required=true, doc="Output file (sam or bam) for improved (realigned) indel related reads") public String OUT2; - @Argument(fullName="ControlRun", shortName="paranoid", required=false, defaultValue="false", doc="If true, all reads that would be otherwise picked and processed by this tool will be saved, unmodified, into the OutputNormal file") public boolean CONTROL_RUN; + @Argument(fullName="ControlRun", shortName="paranoid", required=false, doc="If true, all reads that would be otherwise picked and processed by this tool will be saved, unmodified, into the OutputNormal file") public boolean CONTROL_RUN = false; @Argument(fullName="ErrorCheckMode", shortName="error", required=false, doc="Error counting mode: MM (mismatches only (from sam tags)), MC (mismatches only doing actual mismatch count on the fly (use this if tags are incorrectly set)), ERR (errors (arachne style: mm+gap lengths)), MG (count mismatches and gaps as one error each)") public String ERR_MODE; - @Argument(fullName="MaxErrors", shortName="maxError", required=false, defaultValue="10000", doc="Maximum number of errors allowed (see ERR_MODE)") public Integer MAX_ERRS; - @Argument(fullName="MaxReadLength", shortName="maxRead", required=false, defaultValue="-1", doc="Ignore reads that are longer than the specified cutoff (not a good way to do things but might be necessary because of performance issues)") public int MAX_READ_LENGTH; + @Argument(fullName="MaxErrors", shortName="maxError", required=false, doc="Maximum number of errors allowed (see ERR_MODE)") public Integer MAX_ERRS = 10000; + @Argument(fullName="MaxReadLength", shortName="maxRead", required=false, doc="Ignore reads that are longer than the specified cutoff (not a good way to do things but might be necessary because of performance issues)") public int MAX_READ_LENGTH = -1; private int discarded_cigar_count = 0; private int discarded_long_read_count = 0; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java index bb6c5624c..967e12b8c 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java @@ -17,10 +17,10 @@ import java.util.List; @WalkerName("IndelIntervals") public class IndelIntervalWalker extends ReadWalker { - @Argument(fullName="maxReadLength", shortName="maxRead", doc="max read length", required=false, defaultValue="-1") - public int maxReadLength; - @Argument(fullName="minIndelsPerInterval", shortName="minIndels", doc="min indels per interval", required=false, defaultValue="1") - public int minIntervalIndelCount; + @Argument(fullName="maxReadLength", shortName="maxRead", doc="max read length", required=false) + public int maxReadLength = -1; + @Argument(fullName="minIndelsPerInterval", shortName="minIndels", doc="min indels per interval", required=false) + public int minIntervalIndelCount = 1; public void initialize() {} diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java index f660ef3cd..773632464 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java @@ -17,8 +17,8 @@ import java.io.File; @WalkerName("IntervalCleaner") public class IntervalCleanerWalker extends LocusWindowWalker { - @Argument(fullName="maxReadLength", shortName="maxRead", doc="max read length", required=false, defaultValue="-1") - public int maxReadLength; + @Argument(fullName="maxReadLength", shortName="maxRead", doc="max read length", required=false) + public int maxReadLength = -1; @Argument(fullName="OutputCleaned", shortName="O", required=true, doc="Output file (sam or bam) for improved (realigned) reads") public String OUT; public static final int MAX_QUAL = 99; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java index 7b8ca424a..516b6d8d0 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java @@ -20,8 +20,8 @@ public class LogisticRecalibrationWalker extends ReadWalker regressors = new HashMap(); private static Logger logger = Logger.getLogger(LogisticRecalibrationWalker.class); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java index aa3fb2ac3..a5b6b2d4f 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java @@ -21,10 +21,10 @@ import edu.mit.broad.picard.PicardException; public class Pilot3CoverageWalker extends LocusWalker { - @Argument(fullName = "extended", shortName="ext", doc="extended output", required=false, defaultValue = "false") - public boolean extendedOutput; + @Argument(fullName = "extended", shortName="ext", doc="extended output", required=false) + public boolean extendedOutput = false; - @Argument(fullName="min_mapq", shortName="mmq", required=false, defaultValue="1", doc="Minimum mapping quality of reads to consider") public Integer MIN_MAPQ; + @Argument(fullName="min_mapq", shortName="mmq", required=false, doc="Minimum mapping quality of reads to consider") public Integer MIN_MAPQ = 1; public void initialize() { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java index 7a348455d..67845a8bb 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java @@ -24,7 +24,7 @@ public class PoolCaller extends LocusWalker List sample_names = null; //@Argument(required=false, shortName="log_metrics", defaultValue="true") public boolean LOG_METRICS; - @Argument(required=false, shortName="fractional_counts", doc="fractional counts", defaultValue="false") public boolean FRACTIONAL_COUNTS; + @Argument(required=false, shortName="fractional_counts", doc="fractional counts") public boolean FRACTIONAL_COUNTS = false; private Random random; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java index 0cdb18f8d..94786e5f1 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java @@ -24,10 +24,10 @@ public class PoolCallingExperiment extends LocusWalker sample_names = null; - @Argument(required=false, shortName="downsample", doc="downsample", defaultValue="4") public int DOWNSAMPLE; - @Argument(required=false, shortName="downsample_noise", doc="downsample noise", defaultValue="3") public int DOWNSAMPLE_NOISE; - @Argument(required=false, shortName="log_metrics", doc="log metrics", defaultValue="true") public boolean LOG_METRICS; - @Argument(required=false, shortName="fractional_counts", doc="fractional counts", defaultValue="false") public boolean FRACTIONAL_COUNTS; + @Argument(required=false, shortName="downsample", doc="downsample") public int DOWNSAMPLE = 4; + @Argument(required=false, shortName="downsample_noise", doc="downsample noise") public int DOWNSAMPLE_NOISE = 3; + @Argument(required=false, shortName="log_metrics", doc="log metrics") public boolean LOG_METRICS = true; + @Argument(required=false, shortName="fractional_counts", doc="fractional counts") public boolean FRACTIONAL_COUNTS = false; private Random random; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java index ae7b6a673..b496768a2 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java @@ -20,9 +20,9 @@ import java.util.Random; * @author Kiran Garimella */ public class ReadErrorRateWalker extends ReadWalker { - @Argument(fullName="printVisualHits", shortName="v", doc="print visual hits", required=false, defaultValue="false") public boolean printVisualHits; - @Argument(fullName="useNextBestBase", shortName="nb", doc="use next best base", required=false, defaultValue="false") public boolean useNextBestBase; - @Argument(fullName="useNextRandomBase", shortName="nr", doc="use next random base", required=false, defaultValue="false") public boolean useNextRandomBase; + @Argument(fullName="printVisualHits", shortName="v", doc="print visual hits", required=false) public boolean printVisualHits = false; + @Argument(fullName="useNextBestBase", shortName="nb", doc="use next best base", required=false) public boolean useNextBestBase = false; + @Argument(fullName="useNextRandomBase", shortName="nr", doc="use next random base", required=false) public boolean useNextRandomBase = false; /** * Ignore reads with indels or clipping diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java index 03ddfa36b..4611faa39 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java @@ -19,15 +19,15 @@ import java.util.*; // j.maguire 3-7-2009 public class SingleSampleGenotyper extends LocusWalker { - @Argument(fullName="metrics", shortName="met", doc="metrics", required=false, defaultValue="/dev/null") public String metricsFileName; - @Argument(fullName="metInterval", shortName="mi", doc="metInterval", required=false, defaultValue="50000") public Integer metricsInterval; - @Argument(fullName="printMetrics", shortName="printMetrics", doc="printMetrics", required=false, defaultValue="true") public Boolean printMetrics; - @Argument(fullName="lodThreshold", shortName="lod", doc="lodThreshold", required=false, defaultValue="5.0") public Double lodThreshold; - @Argument(fullName="fourBaseMode", shortName="fb", doc="fourBaseMode", required=false, defaultValue="false") public Boolean fourBaseMode; - @Argument(fullName="retest", shortName="re", doc="retest", required=false, defaultValue="false") public Boolean retest; - @Argument(fullName="qHom", shortName="qHom", doc="qHom", required=false, defaultValue="0.04") public Double qHom; - @Argument(fullName="qHet", shortName="qHet", doc="qHet", required=false, defaultValue="0.49") public Double qHet; - @Argument(fullName="qHomNonRef", shortName="qHomNonRef", doc="qHomNonRef", required=false, defaultValue="0.97") public Double qHomNonRef; + @Argument(fullName="metrics", shortName="met", doc="metrics", required=false) public String metricsFileName = "/dev/null"; + @Argument(fullName="metInterval", shortName="mi", doc="metInterval", required=false) public Integer metricsInterval = 50000; + @Argument(fullName="printMetrics", shortName="printMetrics", doc="printMetrics", required=false) public Boolean printMetrics = true; + @Argument(fullName="lodThreshold", shortName="lod", doc="lodThreshold", required=false) public Double lodThreshold = 5.0; + @Argument(fullName="fourBaseMode", shortName="fb", doc="fourBaseMode", required=false) public Boolean fourBaseMode = false; + @Argument(fullName="retest", shortName="re", doc="retest", required=false) public Boolean retest = false; + @Argument(fullName="qHom", shortName="qHom", doc="qHom", required=false) public Double qHom = 0.04; + @Argument(fullName="qHet", shortName="qHet", doc="qHet", required=false) public Double qHet = 0.49; + @Argument(fullName="qHomNonRef", shortName="qHomNonRef", doc="qHomNonRef", required=false) public Double qHomNonRef = 0.97; public AlleleMetrics metrics; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java index 16d93c3a3..81ef7ac89 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java @@ -27,8 +27,8 @@ public class SomaticCoverageWalker extends LocusWalker { @Argument(fullName = "normal_sample_name", shortName = "s2", doc="normal sample name", required = true) public String normalSampleName; - @Argument(fullName = "extended", shortName="ext", doc="extended output", required=false, defaultValue = "false") - public boolean extendedOutput; + @Argument(fullName = "extended", shortName="ext", doc="extended output", required=false) + public boolean extendedOutput = false; // --normal_sample_name TCGA-06-0188-10B-01W --tumor_sample_name TCGA-06-0188-01A-01W diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/Argument.java b/java/src/org/broadinstitute/sting/utils/cmdLine/Argument.java index a64cd1fa3..5e951167f 100755 --- a/java/src/org/broadinstitute/sting/utils/cmdLine/Argument.java +++ b/java/src/org/broadinstitute/sting/utils/cmdLine/Argument.java @@ -59,10 +59,4 @@ public @interface Argument { * argument should be independent. */ String exclusive() default ""; - - /** - * What is the default value for this argument type. - * @return Default value of this argument type. - */ - String defaultValue() default ""; }