Should have checked in
This commit is contained in:
Mark DePristo
parent
e2c066ac1e
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49e831a13b
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@ -51,8 +51,66 @@ import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import java.util.regex.Pattern;
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/**
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/**
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* This ReadWalker provides simple, yet powerful read clipping capabilities. It allows the user to clip bases in reads
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* This tool provides simple, powerful read clipping capabilities.
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*
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* <p>
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* It allows the user to clip bases in reads
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* with poor quality scores, that match particular sequences, or that were generated by particular machine cycles.
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* with poor quality scores, that match particular sequences, or that were generated by particular machine cycles.
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* </p>
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*
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* <h2>Input</h2>
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* <p>
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* A BAM file containing.
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* </p>
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*
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* <h2>Output</h2>
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* <p>
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* <ul>
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* <li>-o: a OutputFormatted (recommended BED) file with the callable status covering each base</li>
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* <li>-summary: a table of callable status x count of all examined bases</li>
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* </ul>
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* </p>
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*
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* <h2>Examples</h2>
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* <pre>
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* -T CallableLociWalker \
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* -I my.bam \
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* -summary my.summary \
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* -o my.bed
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* </pre>
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*
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* would produce a BED file (my.bed) that looks like:
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*
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* <pre>
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* 20 10000000 10000864 CALLABLE
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* 20 10000865 10000985 POOR_MAPPING_QUALITY
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* 20 10000986 10001138 CALLABLE
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* 20 10001139 10001254 POOR_MAPPING_QUALITY
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* 20 10001255 10012255 CALLABLE
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* 20 10012256 10012259 POOR_MAPPING_QUALITY
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* 20 10012260 10012263 CALLABLE
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* 20 10012264 10012328 POOR_MAPPING_QUALITY
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* 20 10012329 10012550 CALLABLE
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* 20 10012551 10012551 LOW_COVERAGE
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* 20 10012552 10012554 CALLABLE
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* 20 10012555 10012557 LOW_COVERAGE
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* 20 10012558 10012558 CALLABLE
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* et cetera...
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* </pre>
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* as well as a summary table that looks like:
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*
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* <pre>
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* state nBases
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* REF_N 0
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* CALLABLE 996046
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* NO_COVERAGE 121
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* LOW_COVERAGE 928
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* EXCESSIVE_COVERAGE 0
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* POOR_MAPPING_QUALITY 2906
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* </pre>
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*
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* @author Mark DePristo
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* @since May 7, 2010
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*/
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*/
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@Requires({DataSource.READS})
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@Requires({DataSource.READS})
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public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithData, ClipReadsWalker.ClippingData> {
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public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithData, ClipReadsWalker.ClippingData> {
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@ -0,0 +1,115 @@
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/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.qc;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.*;
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/**
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* Summary test
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*
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* <p>Body test</p>
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*/
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public class DocumentationTest extends RodWalker<Integer, Integer> {
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// the docs for the arguments are in the collection
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@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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/**
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* dbSNP comparison VCF. By default, the dbSNP file is used to specify the set of "known" variants.
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* Other sets can be specified with the -knownName (--known_names) argument.
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*/
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@ArgumentCollection
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protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
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/**
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* detailed documentation about the argument goes here.
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*/
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@Input(fullName="listofRodBinding", shortName = "disc", doc="Output variants that were not called in this Feature comparison track", required=false)
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private List<RodBinding<VariantContext>> listOfRodBinding = Collections.emptyList();
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@Input(fullName="optionalRodBinding", shortName = "conc", doc="Output variants that were also called in this Feature comparison track", required=false)
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private RodBinding<VariantContext> concordanceTrack;
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@Input(fullName="optionalRodBindingWithoutDefault", shortName = "optionalRodBindingWithoutDefault", doc="Output variants that were also called in this Feature comparison track", required=false)
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private RodBinding<VariantContext> noDefaultOptionalRodBinding;
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@Input(fullName="optionalRodBindingWithoutDefaultNull", shortName = "shortTest", doc="Output variants that were also called in this Feature comparison track", required=false)
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private RodBinding<VariantContext> noDefaultOptionalRodBindingNull = null;
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@Input(fullName="featureArg", shortName = "featureArg", doc="A RodBinding of feature", required=false)
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private RodBinding<Feature> featureArg = null;
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@Output(doc="VCFWriter",required=true)
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protected VCFWriter vcfWriter = null;
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@Advanced
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@Argument(fullName="setString", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false)
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public Set<String> sampleNames;
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@Argument(fullName="setStringInitialized", shortName="setStringInitialized", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false)
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public Set<String> setStringInitialized = new HashSet<String>();
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@Argument(shortName="optionalArgWithMissinglessDefault", doc="One or more criteria to use when selecting the data. Evaluated *after* the specified samples are extracted and the INFO-field annotations are updated.", required=false)
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public ArrayList<String> SELECT_EXPRESSIONS = new ArrayList<String>();
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@Argument(shortName="AAAAA", fullName = "AAAAA", doc="Should be the first argument", required=false)
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public boolean FIRST_ARG = false;
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@Advanced
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@Argument(fullName="booleanArg", shortName="env", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
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private boolean EXCLUDE_NON_VARIANTS = false;
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@Advanced
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@Argument(fullName="booleanArray", shortName="booleanArray", doc="x", required=false)
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private boolean[] boolArray = null;
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@Argument(fullName="enumTest", shortName="enumTest", doc="Test enum", required=false)
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private TestEnum TestEnumArg = TestEnum.ENUM2;
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public enum TestEnum {
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/** Docs for enum1 */
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ENUM1,
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/** Docs for enum2 */
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ENUM2
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}
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@Hidden
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@Argument(fullName="hiddenArg", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
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private boolean KEEP_AF_SPECTRUM = false;
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; }
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) { return value + sum; }
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public void onTraversalDone(Integer result) { }
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}
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