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Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@598 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-05 22:43:40 +00:00
parent ec0261275b
commit b0cdba8bb3
20 changed files with 56 additions and 56 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
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@ -15,7 +15,7 @@ import java.util.List;
* To change this template use File | Settings | File Templates.
*/
public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>> {
@Argument(fullName="suppressLocusPrinting",required=false,defaultValue="false")
@Argument(fullName="suppressLocusPrinting",doc="Suppress printing",required=false,defaultValue="false")
public boolean suppressPrinting;
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {

4
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -15,10 +15,10 @@ import org.broadinstitute.sting.utils.ReadBackedPileup;
* To change this template use File | Settings | File Templates.
*/
public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
@Argument(fullName="verbose",required=false,defaultValue="false")
@Argument(fullName="verbose",doc="verbose",required=false,defaultValue="false")
public boolean VERBOSE;
@Argument(fullName="extended",shortName="ext",required=false,defaultValue="false")
@Argument(fullName="extended",shortName="ext",doc="extended",required=false,defaultValue="false")
public boolean EXTENDED;
public boolean FLAG_UNCOVERED_BASES = true; // todo: how do I make this a command line argument?

2
java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
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@ -17,7 +17,7 @@ import org.broadinstitute.sting.utils.ReadBackedPileup;
* To change this template use File | Settings | File Templates.
*/
public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats> {
@Argument(fullName="continue_after_error",required=false,defaultValue="false")
@Argument(fullName="continue_after_error",doc="Continue after an error",required=false,defaultValue="false")
public boolean CONTINUE_AFTER_AN_ERROR;
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
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@ -21,7 +21,7 @@ import java.io.DataInputStream;
public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate, String>// implements AllelicVariant
{
@Argument(doc="Number of chromosomes in data") public int N;
@Argument(required=false,defaultValue="0") public int DOWNSAMPLE;
@Argument(required=false,doc="downsample",defaultValue="0") public int DOWNSAMPLE;
@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;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java
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@ -15,10 +15,10 @@ import java.io.FileNotFoundException;
@WalkerName("CountCovariates")
public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName="MAX_READ_LENGTH", shortName="mrl", required=false,defaultValue="101")
@Argument(fullName="MAX_READ_LENGTH", shortName="mrl", doc="max read length", required=false,defaultValue="101")
public int MAX_READ_LENGTH;
@Argument(fullName="MAX_QUAL_SCORE", shortName="mqs", required=false,defaultValue="63")
@Argument(fullName="MAX_QUAL_SCORE", shortName="mqs", doc="max quality score", required=false,defaultValue="63")
public int MAX_QUAL_SCORE;
@Argument(fullName="OUTPUT_FILEROOT", shortName="outroot", required=false, defaultValue="output", doc="Filename root for the outputted logistic regression training files")

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/FindNonrandomSecondBestBasePiles.java
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@ -21,7 +21,7 @@ import java.util.List;
import java.util.ArrayList;
public class FindNonrandomSecondBestBasePiles extends LocusWalker<Integer, Integer> {
@Argument(fullName="verbose",required=false,defaultValue="false")
@Argument(fullName="verbose",doc="verbose",required=false,defaultValue="false")
public boolean VERBOSE;
private AlleleFrequencyWalker caller_1b;

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java
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@ -24,13 +24,13 @@ import java.io.File;
* @author Kiran Garimella
*/
public class IOCrusherWalker extends ReadWalker<SAMRecord, ArrayList<SAMFileWriter>> {
@Argument(shortName="nWaysOut",required=false,defaultValue="1")
@Argument(shortName="nWaysOut",doc="n ways out",required=false,defaultValue="1")
public int nWaysOut;
@Argument(shortName="readScaling",required=false,defaultValue="1")
@Argument(shortName="readScaling",doc="read scaling",required=false,defaultValue="1")
public float readScaling;
@Argument(shortName="outputBase", required=true)
@Argument(shortName="outputBase",doc="output base",required=true)
public String outputBase;
public long nReadsRead = 0;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java
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@ -17,9 +17,9 @@ import java.util.List;
@WalkerName("IndelIntervals")
public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval, IndelIntervalWalker.Interval> {
@Argument(fullName="maxReadLength", shortName="maxRead", required=false, defaultValue="-1")
@Argument(fullName="maxReadLength", shortName="maxRead", doc="max read length", required=false, defaultValue="-1")
public int maxReadLength;
@Argument(fullName="minIndelsPerInterval", shortName="minIndels", required=false, defaultValue="1")
@Argument(fullName="minIndelsPerInterval", shortName="minIndels", doc="min indels per interval", required=false, defaultValue="1")
public int minIntervalIndelCount;
public void initialize() {}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
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@ -19,7 +19,7 @@ import java.io.File;
@WalkerName("IntervalCleaner")
public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer> {
@Argument(fullName="maxReadLength", shortName="maxRead", required=false, defaultValue="-1")
@Argument(fullName="maxReadLength", shortName="maxRead", doc="max read length", required=false, defaultValue="-1")
public int maxReadLength;
@Argument(fullName="OutputCleaned", shortName="O", required=true, doc="Output file (sam or bam) for improved (realigned) reads")
public String OUT;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java
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@ -17,10 +17,10 @@ import java.io.FileNotFoundException;
@WalkerName("LogisticRecalibration")
public class LogisticRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
@Argument(shortName="logisticParams", required=true)
@Argument(shortName="logisticParams", doc="logistic params file", required=true)
public String logisticParamsFile;
@Argument(shortName="outputBAM", required=false, defaultValue="")
@Argument(shortName="outputBAM", doc="output BAM file", required=false, defaultValue="")
public String outputFile;
HashMap<String, LogisticRegressor> regressors = new HashMap<String, LogisticRegressor>();

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
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@ -14,9 +14,9 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord, TrioConcordanceRecord> {
@Argument(fullName="consensus_cutoff", shortName="XC",required=true ) public Double CONS_CUTOFF;
@Argument(fullName="snp_cutoff", shortName="XS",required=true ) public Double SNP_CUTOFF;
@Argument(fullName="indel_cutoff", shortName="XI",required=true ) public Double INDEL_CUTOFF;
@Argument(fullName="consensus_cutoff", shortName="XC", doc="consensus cutoff", required=true ) public Double CONS_CUTOFF;
@Argument(fullName="snp_cutoff", shortName="XS", doc="snp cutoff", required=true ) public Double SNP_CUTOFF;
@Argument(fullName="indel_cutoff", shortName="XI", doc="indel cutoff", required=true ) public Double INDEL_CUTOFF;
@Argument(fullName="log_concordant", shortName="LC",doc="If set, all trio-concordant sites will be logged at level INFO") public boolean LOG_CONCORDANT;
@Argument(fullName="log_discordant", shortName="LD",doc="If set, all trio-discordant sites will be logged at level INFO") public boolean LOG_DISCORDANT;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java
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@ -21,7 +21,7 @@ import edu.mit.broad.picard.PicardException;
public class Pilot3CoverageWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName = "extended", shortName="ext", required=false, defaultValue = "false")
@Argument(fullName = "extended", shortName="ext", doc="extended output", required=false, defaultValue = "false")
public boolean extendedOutput;
@Argument(fullName="min_mapq", shortName="mmq", required=false, defaultValue="1", doc="Minimum mapping quality of reads to consider") public Integer MIN_MAPQ;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
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@ -24,7 +24,7 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
List<String> sample_names = null;
//@Argument(required=false, shortName="log_metrics", defaultValue="true") public boolean LOG_METRICS;
@Argument(required=false, shortName="fractional_counts", defaultValue="false") public boolean FRACTIONAL_COUNTS;
@Argument(required=false, shortName="fractional_counts", doc="fractional counts", defaultValue="false") public boolean FRACTIONAL_COUNTS;
private Random random;

8
java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java
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@ -24,10 +24,10 @@ public class PoolCallingExperiment extends LocusWalker<AlleleFrequencyEstimate,
AlleleFrequencyWalker pooled_caller = null;
List<String> sample_names = null;
@Argument(required=false, shortName="downsample", defaultValue="4") public int DOWNSAMPLE;
@Argument(required=false, shortName="downsample_noise", defaultValue="3") public int DOWNSAMPLE_NOISE;
@Argument(required=false, shortName="log_metrics", defaultValue="true") public boolean LOG_METRICS;
@Argument(required=false, shortName="fractional_counts", defaultValue="false") public boolean FRACTIONAL_COUNTS;
@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;
private Random random;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java
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@ -20,7 +20,7 @@ import edu.mit.broad.picard.PicardException;
public class PopPriorWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName = "quality_score_cutoff", required = false) public Byte qualityScoreCutoff;
@Argument(fullName = "quality_score_cutoff", doc="quality score cutoff", required = false) public Byte qualityScoreCutoff;
public PopPriorWalker() {
}

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java
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@ -20,9 +20,9 @@ import java.util.Random;
* @author Kiran Garimella
*/
public class ReadErrorRateWalker extends ReadWalker<boolean[], int[]> {
@Argument(fullName="printVisualHits", shortName="v", required=false, defaultValue="false") public boolean printVisualHits;
@Argument(fullName="useNextBestBase", shortName="nb", required=false, defaultValue="false") public boolean useNextBestBase;
@Argument(fullName="useNextRandomBase", shortName="nr", required=false, defaultValue="false") public boolean useNextRandomBase;
@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;
/**
* Ignore reads with indels or clipping

18
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
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@ -19,15 +19,15 @@ import java.util.*;
// j.maguire 3-7-2009
public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate, Integer> {
@Argument(fullName="metrics", shortName="met", required=false, defaultValue="/dev/null") public String metricsFileName;
@Argument(fullName="metInterval", shortName="mi", required=false, defaultValue="50000") public Integer metricsInterval;
@Argument(fullName="printMetrics", shortName="printMetrics", required=false, defaultValue="true") public Boolean printMetrics;
@Argument(fullName="lodThreshold", shortName="lod", required=false, defaultValue="5.0") public Double lodThreshold;
@Argument(fullName="fourBaseMode", shortName="fb", required=false, defaultValue="false") public Boolean fourBaseMode;
@Argument(fullName="retest", shortName="re", required=false, defaultValue="false") public Boolean retest;
@Argument(fullName="qHom", shortName="qHom", required=false, defaultValue="0.04") public Double qHom;
@Argument(fullName="qHet", shortName="qHet", required=false, defaultValue="0.49") public Double qHet;
@Argument(fullName="qHomNonRef", shortName="qHomNonRef", required=false, defaultValue="0.97") public Double qHomNonRef;
@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;
public AlleleMetrics metrics;

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
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@ -21,13 +21,13 @@ import edu.mit.broad.picard.PicardException;
public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName = "tumor_sample_name", shortName = "s1", required = true)
@Argument(fullName = "tumor_sample_name", shortName = "s1", doc="tumor sample name", required = true)
public String tumorSampleName;
@Argument(fullName = "normal_sample_name", shortName = "s2", required = true)
@Argument(fullName = "normal_sample_name", shortName = "s2", doc="normal sample name", required = true)
public String normalSampleName;
@Argument(fullName = "extended", shortName="ext", required=false, defaultValue = "false")
@Argument(fullName = "extended", shortName="ext", doc="extended output", required=false, defaultValue = "false")
public boolean extendedOutput;

2
java/src/org/broadinstitute/sting/utils/cmdLine/Argument.java
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@ -42,7 +42,7 @@ public @interface Argument {
* --help argument is specified.
* @return Doc string associated with this command-line argument.
*/
String doc() default "";
String doc();
/**
* Is this command-line argument required. The application should exit

28
java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java
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@ -33,7 +33,7 @@ public class ParsingEngineTest extends BaseTest {
}
private class InputFileArgProvider {
@Argument(fullName="input_file",shortName="I")
@Argument(fullName="input_file",doc="input file",shortName="I")
public String inputFile;
}
@ -81,7 +81,7 @@ public class ParsingEngineTest extends BaseTest {
private class MultiCharShortNameArgProvider {
@Argument(shortName="out")
@Argument(shortName="out", doc="output file")
public String outputFile;
}
@ -128,7 +128,7 @@ public class ParsingEngineTest extends BaseTest {
}
private class AllLociArgProvider {
@Argument(fullName="all_loci",shortName="A")
@Argument(fullName="all_loci",shortName="A", doc="all loci")
public boolean allLoci = false;
}
@ -149,7 +149,7 @@ public class ParsingEngineTest extends BaseTest {
}
private class MultiValueArgProvider {
@Argument(fullName="input_file",shortName="I")
@Argument(fullName="input_file",shortName="I", doc="input file")
public String[] inputFile;
}
@ -174,7 +174,7 @@ public class ParsingEngineTest extends BaseTest {
}
private class IntegerListArgProvider {
@Argument(fullName="integer_list",shortName="N")
@Argument(fullName="integer_list",shortName="N",doc="integer list")
public List<Integer> integers;
}
@ -199,7 +199,7 @@ public class ParsingEngineTest extends BaseTest {
}
private class UntypedListArgProvider {
@Argument(fullName="untyped_list",shortName="N")
@Argument(fullName="untyped_list",shortName="N", doc="untyped list")
public List integers;
}
@ -213,7 +213,7 @@ public class ParsingEngineTest extends BaseTest {
}
private class RequiredArgProvider {
@Argument(required=true)
@Argument(required=true,doc="value")
public Integer value;
}
@ -232,7 +232,7 @@ public class ParsingEngineTest extends BaseTest {
}
private class UnrequiredArgProvider {
@Argument(required=false)
@Argument(required=false,doc="unrequired value")
public Integer value;
}
@ -251,10 +251,10 @@ public class ParsingEngineTest extends BaseTest {
}
private class DuplicateLongNameProvider {
@Argument(fullName="myarg")
@Argument(fullName="myarg",doc="my arg")
public Integer foo;
@Argument(fullName="myarg")
@Argument(fullName="myarg", doc="my arg")
public Integer bar;
}
@ -265,10 +265,10 @@ public class ParsingEngineTest extends BaseTest {
private class DuplicateShortNameProvider {
@Argument(shortName="myarg")
@Argument(shortName="myarg", doc="my arg")
public Integer foo;
@Argument(shortName="myarg")
@Argument(shortName="myarg", doc="my arg")
public Integer bar;
}
@ -327,7 +327,7 @@ public class ParsingEngineTest extends BaseTest {
}
private class PackageProtectedArgProvider {
@Argument
@Argument(doc="foo")
Integer foo;
}
@ -342,7 +342,7 @@ public class ParsingEngineTest extends BaseTest {
}
private class CamelCaseArgProvider {
@Argument
@Argument(doc="my arg")
Integer myArg;
}
}