From 49e831a13b51dc37877138dfca4e0cd178f4f4e5 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 19 Aug 2011 14:35:16 -0400 Subject: [PATCH] Should have checked in --- .../sting/gatk/walkers/ClipReadsWalker.java | 60 ++++++++- .../gatk/walkers/qc/DocumentationTest.java | 115 ++++++++++++++++++ 2 files changed, 174 insertions(+), 1 deletion(-) create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java index 76b0276cd..68afed296 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java @@ -51,8 +51,66 @@ import java.util.regex.Matcher; import java.util.regex.Pattern; /** - * This ReadWalker provides simple, yet powerful read clipping capabilities. It allows the user to clip bases in reads + * This tool provides simple, 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. + *

+ * + *

Input

+ *

+ * A BAM file containing. + *

+ * + *

Output

+ *

+ *

+ *

+ * + *

Examples

+ * 
+ *     -T CallableLociWalker \
+ *     -I my.bam \
+ *     -summary my.summary \
+ *     -o my.bed
+ *
+ * + * would produce a BED file (my.bed) that looks like: + * + * 
+ *     20 10000000 10000864 CALLABLE
+ *     20 10000865 10000985 POOR_MAPPING_QUALITY
+ *     20 10000986 10001138 CALLABLE
+ *     20 10001139 10001254 POOR_MAPPING_QUALITY
+ *     20 10001255 10012255 CALLABLE
+ *     20 10012256 10012259 POOR_MAPPING_QUALITY
+ *     20 10012260 10012263 CALLABLE
+ *     20 10012264 10012328 POOR_MAPPING_QUALITY
+ *     20 10012329 10012550 CALLABLE
+ *     20 10012551 10012551 LOW_COVERAGE
+ *     20 10012552 10012554 CALLABLE
+ *     20 10012555 10012557 LOW_COVERAGE
+ *     20 10012558 10012558 CALLABLE
+ *     et cetera...
+ *
+ * as well as a summary table that looks like: + * + * 
+ *                        state nBases
+ *                        REF_N 0
+ *                     CALLABLE 996046
+ *                  NO_COVERAGE 121
+ *                 LOW_COVERAGE 928
+ *           EXCESSIVE_COVERAGE 0
+ *         POOR_MAPPING_QUALITY 2906
+ *
+ * + * @author Mark DePristo + * @since May 7, 2010 */ @Requires({DataSource.READS}) public class ClipReadsWalker extends ReadWalker { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java new file mode 100644 index 000000000..933e24784 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java @@ -0,0 +1,115 @@ +/* + * Copyright (c) 2011, 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. + */ + +package org.broadinstitute.sting.gatk.walkers.qc; + +import org.broad.tribble.Feature; +import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; +import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.util.*; + +/** + * Summary test + * + *

Body test

+ */ +public class DocumentationTest extends RodWalker { + // the docs for the arguments are in the collection + @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + + /** + * dbSNP comparison VCF. By default, the dbSNP file is used to specify the set of "known" variants. + * Other sets can be specified with the -knownName (--known_names) argument. + */ + @ArgumentCollection + protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection(); + + /** + * detailed documentation about the argument goes here. + */ + @Input(fullName="listofRodBinding", shortName = "disc", doc="Output variants that were not called in this Feature comparison track", required=false) + private List> listOfRodBinding = Collections.emptyList(); + + @Input(fullName="optionalRodBinding", shortName = "conc", doc="Output variants that were also called in this Feature comparison track", required=false) + private RodBinding concordanceTrack; + + @Input(fullName="optionalRodBindingWithoutDefault", shortName = "optionalRodBindingWithoutDefault", doc="Output variants that were also called in this Feature comparison track", required=false) + private RodBinding noDefaultOptionalRodBinding; + + @Input(fullName="optionalRodBindingWithoutDefaultNull", shortName = "shortTest", doc="Output variants that were also called in this Feature comparison track", required=false) + private RodBinding noDefaultOptionalRodBindingNull = null; + + @Input(fullName="featureArg", shortName = "featureArg", doc="A RodBinding of feature", required=false) + private RodBinding featureArg = null; + + @Output(doc="VCFWriter",required=true) + protected VCFWriter vcfWriter = null; + + @Advanced + @Argument(fullName="setString", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false) + public Set sampleNames; + + @Argument(fullName="setStringInitialized", shortName="setStringInitialized", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false) + public Set setStringInitialized = new HashSet(); + + @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) + public ArrayList SELECT_EXPRESSIONS = new ArrayList(); + + @Argument(shortName="AAAAA", fullName = "AAAAA", doc="Should be the first argument", required=false) + public boolean FIRST_ARG = false; + + @Advanced + @Argument(fullName="booleanArg", shortName="env", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false) + private boolean EXCLUDE_NON_VARIANTS = false; + + @Advanced + @Argument(fullName="booleanArray", shortName="booleanArray", doc="x", required=false) + private boolean[] boolArray = null; + + @Argument(fullName="enumTest", shortName="enumTest", doc="Test enum", required=false) + private TestEnum TestEnumArg = TestEnum.ENUM2; + public enum TestEnum { + /** Docs for enum1 */ + ENUM1, + /** Docs for enum2 */ + ENUM2 + } + + @Hidden + @Argument(fullName="hiddenArg", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false) + private boolean KEEP_AF_SPECTRUM = false; + + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; } + public Integer reduceInit() { return 0; } + public Integer reduce(Integer value, Integer sum) { return value + sum; } + public void onTraversalDone(Integer result) { } +}