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

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java

@@ -103,9 +103,7 @@ public class CleanedReadInjector extends ReadWalker<Integer,Integer> {
 
         String uniquifiedReadName = getUniquifiedReadName(read);
         if ( !cleanedReadHash.contains(uniquifiedReadName) )
-        {
             outputBAM.addAlignment(read);
-        }
         return cleanedReadCount;
     }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java

@@ -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;

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelIntervalWalker.java

@@ -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() {}
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java

@@ -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;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalMergerWalker.java

@@ -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;

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java

@@ -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;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/SNPClusterWalker.java

@@ -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)