diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java index 0f8b4ef15..74c49d44b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java @@ -103,9 +103,7 @@ public class CleanedReadInjector extends ReadWalker { String uniquifiedReadName = getUniquifiedReadName(read); if ( !cleanedReadHash.contains(uniquifiedReadName) ) - { outputBAM.addAlignment(read); - } return cleanedReadCount; } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java index 686caf148..0932345cc 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java @@ -20,28 +20,28 @@ import java.util.Set; public class IndelGenotyperWalker extends ReadWalker { @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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelIntervalWalker.java index 144f2fb79..bb5ca3ddb 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelIntervalWalker.java +++ b/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 { @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() {} diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java index 562b01459..2b4df3325 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java +++ b/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 { @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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalMergerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalMergerWalker.java index 090375613..f80557da2 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalMergerWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalMergerWalker.java @@ -44,9 +44,9 @@ public class IntervalMergerWalker extends ReadWalker { @Argument(fullName="intervalsToMerge", shortName="intervals", doc="Intervals to merge", required=true) List 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 intervals; private GenomeLoc firstInterval = null; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java index fe30c3cb1..3c502a3f8 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java +++ b/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>> { @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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/SNPClusterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/SNPClusterWalker.java index b407c4de7..64c0965bd 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/SNPClusterWalker.java +++ b/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 { @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)