diff --git a/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java b/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java index 54eaa7e90..7ed7f9003 100644 --- a/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java +++ b/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java @@ -9,6 +9,9 @@ import org.broadinstitute.sting.utils.pileup.*; import java.util.*; +/** + * Computes the coverage per sample. + */ public class CoverageBySample extends LocusWalker { private HashSet sampleNames = new HashSet(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 31d3d7c12..bc28c1148 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -15,7 +15,7 @@ import java.io.*; /** - * VariantAnnotator annotates variants. + * Annotates variant calls with context information. Users can specify which of the available annotations to use. */ //@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=VariationRod.class)) @Allows(value={DataSource.READS, DataSource.REFERENCE}) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java index 2fd6bfe47..2b4f478fc 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java @@ -13,7 +13,8 @@ import java.util.*; /** - * CallsetConcordanceWalker finds the concordance between multiple VCF callsets (different tests are available). + * Determines the concordance between multiple VCF call sets at each position. + * Users can specify which concordance tests should be run. */ @Requires(value={DataSource.REFERENCE}) @Reference(window=@Window(start=-20,stop=20)) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java index a6b0b759f..037a8a0d1 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java @@ -5,15 +5,16 @@ import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.utils.cmdLine.Argument; +/** + * Computes the coverage per every bases on the reference, or on the subset of the reference + * specified by the intervals provided. Moving to the next contig on the reference will always restart the + * count anew, even if the count of bases in the last chunk on the previous contig did not reach specified . + */ public class CoarseCoverageWalker extends ReadWalker { - @Argument(fullName="granularity",shortName="G",doc="Will print numbers of reads per every bases "+ - "on the reference, or on the subset of the reference specified by Intervals (if given). Moving to the next "+ - "contig on the reference will always restart the count anew, even if the count of bases in the last chunk on"+ - " the previous contig did not reach specified .",required=true) + @Argument(fullName="granularity", shortName="G", doc="Granularity", required=true) public Integer N; - private int chunkStart = 1; // start of the current chunk we are counting reads for private int contig = 0; // current contig we are on private int count = 0; // number of reads overlapping with the current chunk diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java index 86effd9be..9b4d562db 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java @@ -9,6 +9,9 @@ import org.broadinstitute.sting.utils.genotype.Variation; import java.util.Iterator; +/** + * Create a mask for use with the PickSequenomProbes walker. + */ public class CreateSequenomMask extends RodWalker { public void initialize() {} diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index af8d65861..9c48be440 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java @@ -12,8 +12,9 @@ import java.io.*; import java.util.Iterator; /** - * Generates an alternative reference sequence over the specified interval. Given a variant ROD track (named "snpmask"), - * it replaces the reference bases at variation sites with the bases supplied by the ROD. + * Generates an alternative reference sequence over the specified interval. Given variant ROD tracks, + * it replaces the reference bases at variation sites with the bases supplied by the ROD(s). Additionally, + * allows for a "snpmask" ROD to set overlapping bases to 'N'. */ @WalkerName("FastaAlternateReferenceMaker") @Requires(value={DataSource.REFERENCE}) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 16237feeb..a75925618 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -44,6 +44,10 @@ import java.io.File; import java.util.*; +/** + * A variant caller which unifies the approaches of several disparate callers. Works for single-sample, + * multi-sample, and pooled data. The user can choose from several different incorporated calculation models. + */ @Reference(window=@Window(start=-20,stop=20)) public class UnifiedGenotyper extends LocusWalker>, Integer> { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java index e599952f9..1452bcda2 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java @@ -24,8 +24,8 @@ import java.util.*; */ /** - * Copies reads from the input stream into the outputBAM, replacing those - * reads which have been cleaned with their new clean copies. + * Copies reads from the input stream into the outputBAM, replacing those + * reads which have been cleaned/realigned with their new clean copies. */ @Requires({DataSource.READS, DataSource.REFERENCE}) public class CleanedReadInjector extends ReadWalker { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelIntervalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelIntervalWalker.java index 1abc7d1fa..79bfd6d73 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelIntervalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelIntervalWalker.java @@ -10,11 +10,9 @@ import net.sf.samtools.AlignmentBlock; import java.util.List; -// A walker to determine intervals within which reads should be cleaned and realigned -// because they contain one or more indels (which possibly caused them not to align perfectly). -// Note that the reduce step assumes that reductions occur in order (i.e. no hierarchical reductions), -// although this can easily be changed if necessary. - +/** + * Emits intervals consisting of indels from the aligned reads. + */ @WalkerName("IndelIntervals") @Requires({DataSource.READS, DataSource.REFERENCE}) @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class}) @@ -48,6 +46,8 @@ public class IndelIntervalWalker extends ReadWalker { @@ -60,8 +64,6 @@ public class IntervalCleanerWalker extends LocusWindowWalker private TreeSet readsToWrite = null; private TreeSet nextSetOfReadsToWrite = null; - private boolean debugOn = false; - public void initialize() { if ( LOD_THRESHOLD < 0.0 ) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java index ef9459fac..3ad0284f6 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java @@ -25,7 +25,6 @@ package org.broadinstitute.sting.gatk.walkers.indels; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.filters.Platform454Filter; import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter; import org.broadinstitute.sting.gatk.walkers.*; @@ -36,7 +35,8 @@ import java.util.*; /** - * Merges intervals based on reads which overlap them. + * Merges sets of intervals based on reads which overlap them; no two intervals in the final list + * will have a read that even partially spans them both. A maximum interval size is enforced though. */ @WalkerName("IntervalMerger") @Requires({DataSource.READS, DataSource.REFERENCE}) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java index af226c9ae..dca4b9bff 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java @@ -14,6 +14,9 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import java.util.*; +/** + * Emits intervals consisting of nearby loci with high mismatch rates. + */ @WalkerName("MismatchIntervals") @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class}) public class MismatchIntervalWalker extends LocusWalker, Pair, GenomeLoc>> { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java index 997edb00b..30ec875de 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java @@ -10,6 +10,9 @@ import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.Variation; +/** + * Given a ROD track SNP calls called "snps", emits intervals consisting of clustered SNPs. + */ @WalkerName("SNPClusters") @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="snps",type= VariationRod.class)}) public class SNPClusterWalker extends RefWalker {