From 05b8782d5f86ababb236676cfb3de69c25ba38d7 Mon Sep 17 00:00:00 2001 From: depristo Date: Sun, 13 Dec 2009 18:40:22 +0000 Subject: [PATCH] Documentation updates. Moved CountX.java walkers to QC git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2345 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/ClipReadsWalker.java | 31 ++----------------- .../walkers/{ => qc}/CountLociWalker.java | 0 .../walkers/{ => qc}/CountReadsWalker.java | 0 .../walkers/{ => qc}/CountRodByRefWalker.java | 4 +-- .../gatk/walkers/{ => qc}/CountRodWalker.java | 4 +-- .../graphalign/GraphReferenceAssessor.java | 5 +++ .../graphalign/GraphReferenceBuilder.java | 4 +++ .../varianteval/VariantEvalWalker.java | 13 +++----- 8 files changed, 19 insertions(+), 42 deletions(-) rename java/src/org/broadinstitute/sting/gatk/walkers/{ => qc}/CountLociWalker.java (100%) rename java/src/org/broadinstitute/sting/gatk/walkers/{ => qc}/CountReadsWalker.java (100%) rename java/src/org/broadinstitute/sting/gatk/walkers/{ => qc}/CountRodByRefWalker.java (91%) rename java/src/org/broadinstitute/sting/gatk/walkers/{ => qc}/CountRodWalker.java (97%) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java index 9bc728440..a35f7484f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java @@ -16,36 +16,9 @@ import java.io.File; import net.sf.samtools.util.StringUtil; -/* - * Copyright (c) 2009 The Broad Institute - * - * Permission is hereby granted, free of charge, to any person - * obtaining a copy of this software and associated documentation - * files (the "Software"), to deal in the Software without - * restriction, including without limitation the rights to use, - * copy, modify, merge, publish, distribute, sublicense, and/or sell - * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, subject to the following - * conditions: - * - * The above copyright notice and this permission notice shall be - * included in all copies or substantial portions of the Software. - * - * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, - * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING - * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR - * OTHER DEALINGS IN THE SOFTWARE. - */ - /** - * This walker prints out the reads from the BAM files provided to the traversal engines. - * It also supports the command line option '-outputBamFile filname', which outputs all the - * reads to a specified BAM file - * The walker now also optionally filters reads based on command line options. + * This ReadWalker provides simple, yet powerful read clipping capabilities. It allows the user to clip bases in reads + * with poor quality scores, that match particular sequences, or that were generated by particular machine cycles. */ @Requires({DataSource.READS}) public class ClipReadsWalker extends ReadWalker { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java similarity index 100% rename from java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java similarity index 100% rename from java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/CountRodByRefWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java similarity index 91% rename from java/src/org/broadinstitute/sting/gatk/walkers/CountRodByRefWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java index 0a3ca4ac2..e0a0916a6 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/CountRodByRefWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java @@ -11,8 +11,8 @@ import java.util.ArrayList; import java.util.List; /** - * A very simple walker that prints out counts of the number of reference ordered data objects are - * each locus. For debugging RefWalkers. + * Prints out counts of the number of reference ordered data objects are + * each locus for debugging RefWalkers. */ public class CountRodByRefWalker extends RefWalker, Long>> { @Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/CountRodWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java similarity index 97% rename from java/src/org/broadinstitute/sting/gatk/walkers/CountRodWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java index c4b2c1342..5dcb14611 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/CountRodWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java @@ -14,8 +14,8 @@ import java.util.Collection; import java.util.LinkedList; /** - * A very simple walker that prints out counts of the number of reference ordered data objects are - * each locus. For debugging RodWalkers. + * Prints out counts of the number of reference ordered data objects are + * each locus for debugging RodWalkers. */ public class CountRodWalker extends RodWalker, Long>> { @Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.java index 844c4778f..13a1fdb83 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.java @@ -25,6 +25,11 @@ import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMRecord; +/** + * A completely experimental read walker that consumes a graphical reference emitted by GraphReferenceBuilder as a + * serialized java object and evaluates the number of mismatches to both the flat reference and the graphical + * reference for each read [Not for public use and will change drastically in the future]. + */ public class GraphReferenceAssessor extends ReadWalker { @Argument(fullName="graphFile", shortName="GF", doc="", required=true) String graphFile = null; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java index abcb24aa0..79b4915f9 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java @@ -25,6 +25,10 @@ import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.picard.reference.ReferenceSequenceFileFactory; import net.sf.samtools.util.StringUtil; +/** + * A completely experimental walker that constructs a graphical reference that incorporates variation from provided + * RODs [Not for public use and will change drastically in the future]. + */ @WalkerName("GraphReferenceBuilder") @Requires(value={DataSource.REFERENCE}) public class GraphReferenceBuilder extends RefWalker { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java index ed32e51ae..05dde87dc 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java @@ -16,14 +16,9 @@ import java.io.PrintStream; import java.util.*; /** - * The Broad Institute - * SOFTWARE COPYRIGHT NOTICE AGREEMENT - * This software and its documentation are copyright 2009 by the - * Broad Institute/Massachusetts Institute of Technology. All rights are reserved. - * - * This software is supplied without any warranty or guaranteed support whatsoever. Neither - * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. - * + * A robust and general purpose tool for characterizing the quality of SNPs, Indels, and other variants that includes basic + * counting, ti/tv, dbSNP% (if -D is provided), concordance to chip or validation data, and will show interesting sites (-V) + * that are FNs, FP, etc. */ @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=ReferenceOrderedDatum.class)}) // right now we have no base variant class for rods, this should change //@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)}) @@ -35,7 +30,7 @@ public class VariantEvalWalker extends RefWalker { @Argument(shortName="printVariants", doc="If true, prints the variants in all of the variant tracks that are examined", required=false) public boolean printVariants = false; - @Argument(shortName="badHWEThreshold", doc="XXX", required=false) + @Argument(shortName="badHWEThreshold", doc="Only sites with deviations froim Hardy-Weinberg equilibrium with P-values < than this threshold are flagged", required=false) public double badHWEThreshold = 1e-3; @Argument(fullName="evalContainsGenotypes", shortName = "G", doc="If true, the input list of variants will be treated as a genotyping file, containing assertions of actual genotype values for a particular person. Analyses that only make sense on at the population level will be disabled, while those operating on genotypes will be enabled", required=false)