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Heads up, everyone: command-line args no longer need to be public. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1143 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-01 16:09:22 +00:00
parent b43d4d909e
commit 5a5103cfd2
7 changed files with 26 additions and 28 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java
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@ -103,9 +103,7 @@ public class CleanedReadInjector extends ReadWalker<Integer,Integer> {
String uniquifiedReadName = getUniquifiedReadName(read);
if ( !cleanedReadHash.contains(uniquifiedReadName) )
{
outputBAM.addAlignment(read);
}
return cleanedReadCount;
}

16
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -20,28 +20,28 @@ import java.util.Set;
public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
@Argument(fullName="bed", shortName="bed", doc="BED output file name", required=true)
public java.io.File bed_file;
java.io.File bed_file;
@Argument(fullName="somatic", shortName="somatic",
doc="Perform somatic calls; two input alignment files must be specified", required=false)
public boolean call_somatic = false;
boolean call_somatic = false;
@Argument(fullName="verbose", shortName="verbose",
doc="Tell us what you are calling now (printed to stdout)", required=false)
public boolean verbose = false;
boolean verbose = false;
@Argument(fullName="minCoverage", shortName="minCoverage",
doc="must have minCoverage or more reads to call indel; with --somatic this value is applied to tumor sample", required=false)
public int minCoverage = 6;
int minCoverage = 6;
@Argument(fullName="minNormalCoverage", shortName="minNormalCoverage",
doc="used only with --somatic; normal sample must have at least minNormalCoverage or more reads to call germline/somatic indel", required=false)
public int minNormalCoverage = 4;
int minNormalCoverage = 4;
@Argument(fullName="minFraction", shortName="minFraction",
doc="minimum fraction of reads with indels at a site, out of all reads covering the site, required for a call", required=false)
public double minFraction = 0.3;
double minFraction = 0.3;
@Argument(fullName="minConsensusFraction", shortName="minConsensusFraction",
doc="Minimum fraction of reads with indel at the site that must contain consensus indel in order to make the call", required=false)
public double minConsensusFraction = 0.7;
double minConsensusFraction = 0.7;
@Argument(fullName="refseq", shortName="refseq",
doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated as GENOMIC/UTR/INTRON/CODING", required=false)
public String RefseqFileName = null;
String RefseqFileName = null;
private static int WINDOW_SIZE = 200;
private RunningCoverage coverage;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/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="allow454Reads", shortName="454", doc="process 454 reads", required=false)
public boolean allow454 = false;
boolean allow454 = false;
@Argument(fullName="minIndelsPerInterval", shortName="minIndels", doc="min indels per interval", required=false)
public int minIntervalIndelCount = 1;
int minIntervalIndelCount = 1;
public void initialize() {}

20
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -18,25 +18,25 @@ import java.io.FileWriter;
@WalkerName("IntervalCleaner")
public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer> {
@Argument(fullName="allow454Reads", shortName="454", doc="process 454 reads", required=false)
public boolean allow454 = false;
boolean allow454 = false;
@Argument(fullName="OutputCleaned", shortName="O", required=false, doc="Output file (sam or bam) for improved (realigned) reads")
public String OUT = null;
String OUT = null;
@Argument(fullName="OutputIndels", shortName="indels", required=false, doc="Output file (text) for the indels found")
public String OUT_INDELS = null;
String OUT_INDELS = null;
@Argument(fullName="OutputCleanedReadsOnly", shortName="cleanedOnly", doc="print out cleaned reads only (otherwise, all reads within the intervals)", required=false)
public boolean cleanedReadsOnly = false;
boolean cleanedReadsOnly = false;
@Argument(fullName="statisticsFile", shortName="stats", doc="print out statistics (what does or doesn't get cleaned)", required=false)
public String OUT_STATS = null;
String OUT_STATS = null;
@Argument(fullName="SNPsFile", shortName="snps", doc="print out whether mismatching columns do or don't get cleaned out", required=false)
public String OUT_SNPS = null;
String OUT_SNPS = null;
@Argument(fullName="LODThresholdForCleaning", shortName="LOD", doc="LOD threshold above which the cleaner will clean", required=false)
public double LOD_THRESHOLD = 5.0;
double LOD_THRESHOLD = 5.0;
@Argument(fullName="EntropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false)
public double MISMATCH_THRESHOLD = 0.15;
double MISMATCH_THRESHOLD = 0.15;
@Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necessary to improve performance in deep coverage)", required=false)
public int MAX_CONSENSUSES = 30;
int MAX_CONSENSUSES = 30;
@Argument(fullName="maxReadsForConsensuses", shortName="greedy", doc="max reads used for finding the alternate consensuses (necessary to improve performance in deep coverage)", required=false)
public int MAX_READS_FOR_CONSENSUSES = 120;
int MAX_READS_FOR_CONSENSUSES = 120;
public static final int MAX_QUAL = 99;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalMergerWalker.java
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@ -44,9 +44,9 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
@Argument(fullName="intervalsToMerge", shortName="intervals", doc="Intervals to merge", required=true)
List<String> intervalsSource = null;
@Argument(fullName="allow454Reads", shortName="454", doc="process 454 reads", required=false)
public boolean allow454 = false;
boolean allow454 = false;
@Argument(fullName="maxIntervalSize", shortName="maxInterval", doc="max interval size", required=false)
public int maxIntervalSize = 500;
int maxIntervalSize = 500;
private LinkedList<GenomeLoc> intervals;
private GenomeLoc firstInterval = null;

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
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@ -14,11 +14,11 @@ import java.util.*;
@WalkerName("MismatchIntervals")
public class MismatchIntervalWalker extends LocusWalker<Pair<GenomeLoc, Boolean>, Pair<LinkedList<Boolean>, GenomeLoc>> {
@Argument(fullName="windowSize", shortName="window", doc="window size for calculating entropy", required=false)
public int windowSize = 10;
int windowSize = 10;
@Argument(fullName="mismatchFraction", shortName="mismatch", doc="fraction of mismatching base qualities threshold", required=false)
public double mismatchThreshold = 0.15;
double mismatchThreshold = 0.15;
@Argument(fullName="allow454Reads", shortName="454", doc="process 454 reads", required=false)
public boolean allow454 = false;
boolean allow454 = false;
private final int minReadsAtInterval = 4;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/SNPClusterWalker.java
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@ -13,7 +13,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
@Allows(DataSource.REFERENCE)
public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> {
@Argument(fullName="windowSize", shortName="window", doc="window size for calculating clusters", required=false)
public int windowSize = 10;
int windowSize = 10;
public void initialize() {
if ( windowSize < 1)