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Merge pull request #348 from broadinstitute/gg_gatkdoc_fixes 

Gg gatkdoc fixes
This commit is contained in:
Eric Banks 2013-07-26 13:17:51 -07:00
parent f52196496d 3063d82797
commit 678d038c76
10 changed files with 69 additions and 19 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
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@ -70,9 +70,9 @@ public class VariantRecalibratorArgumentCollection {
throw new ReviewedStingException("VariantRecalibrator mode string is unrecognized, input = " + input);
}
@Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only snps (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both snps and indels simultaneously.", required = false)
@Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels (emitting SNPs untouched in the output VCF); and 3.) BOTH for recalibrating both SNPs and indels simultaneously (for testing purposes only, not recommended for general use).", required = false)
public VariantRecalibratorArgumentCollection.Mode MODE = VariantRecalibratorArgumentCollection.Mode.SNP;
@Argument(fullName="maxGaussians", shortName="mG", doc="The maximum number of Gaussians to try during variational Bayes algorithm", required=false)
@Argument(fullName="maxGaussians", shortName="mG", doc="The maximum number of Gaussians to try during variational Bayes algorithm.", required=false)
public int MAX_GAUSSIANS = 10;
@Argument(fullName="maxIterations", shortName="mI", doc="The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected.", required=false)
public int MAX_ITERATIONS = 100;

23
public/java/src/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java
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@ -32,10 +32,23 @@ import org.broadinstitute.sting.commandline.Argument;
* A read filter (transformer) that sets all reads mapping quality to a given value.
*
* <p>
* If a BAM file contains erroneous or missing mapping qualities, this 'filter' will set
* all your mapping qualities to a given value. Default being 60.
* If a BAM file contains erroneous or missing mapping qualities (MAPQ), this read transformer will set all your
* mapping qualities to a given value (see arguments list for default value).
* </p>
*
* <h3>See also</h3>
*
* <p>ReassignOneMappingQualityFilter: reassigns a single MAPQ value, as opposed to all those found in the BAM file.</p>
*
* <h3>Caveats</h3>
*
* <p>Note that due to the order of operations involved in applying filters, it is possible that other read filters
* (determined either at command-line or internally by the tool you are using) will be applied to your data before
* this read transformation can be applied. If one of those other filters acts on the read mapping quality (MAPQ),
* then you may not obtain the expected results. Unfortunately it is currently not possible to change the order of
* operations from command line. To avoid the problem, we recommend applying this filter separately from any other
* analysis, using PrintReads.</p>
*
*
* <h3>Input</h3>
* <p>
@ -50,9 +63,9 @@ import org.broadinstitute.sting.commandline.Argument;
*
* <h3>Examples</h3>
* <pre>
* java
* -jar GenomeAnalysisTK.jar
* -rf ReassignMappingQuality
* java -jar GenomeAnalysisTK.jar \
* -T PrintReads \
* -rf ReassignMappingQuality \
* -DMQ 35
* </pre>
*

7
public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java
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@ -32,7 +32,7 @@ import org.broadinstitute.sting.commandline.Argument;
* A read filter (transformer) that changes a given read mapping quality to a different value.
*
* <p>
* This 'filter' will change a certain read mapping quality to a different value without affecting reads that
* This read transformer will change a certain read mapping quality to a different value without affecting reads that
* have other mapping qualities. This is intended primarily for users of RNA-Seq data handling programs such
* as TopHat, which use MAPQ = 255 to designate uniquely aligned reads. According to convention, 255 normally
* designates "unknown" quality, and most GATK tools automatically ignore such reads. By reassigning a different
@ -46,7 +46,6 @@ import org.broadinstitute.sting.commandline.Argument;
* that have no assigned mapping qualities.
* </p>
*
*
* <h3>Input</h3>
* <p>
* BAM file(s)
@ -60,8 +59,8 @@ import org.broadinstitute.sting.commandline.Argument;
*
* <h3>Examples</h3>
* <pre>
* java
* -jar GenomeAnalysisTK.jar
* java -jar GenomeAnalysisTK.jar
* -T PrintReads
* -rf ReassignOneMappingQuality
* -RMQF 255
* -RMQT 60

7
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -46,7 +46,12 @@ import java.util.Map;
/**
* The allele balance (fraction of ref bases over ref + alt bases) across all biallelic het-called samples
* Allele balance across all samples
*
* <p>The allele balance is the fraction of ref bases over ref + alt bases.</p>
*
* <h3>Caveats</h3>
* <p>Note that this annotation will only work properly for biallelic samples that are called as heterozygous.</p>
*/
public class AlleleBalance extends InfoFieldAnnotation {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -51,7 +51,7 @@ import java.util.List;
* <p>The allele balance is the fraction of ref bases over ref + alt bases.</p>
*
* <h3>Caveats</h3>
* <p>Note that this annotation will only work properly for biallelic het-called samples.</p>
* <p>Note that this annotation will only work properly for biallelic samples that are called as heterozygous.</p>
* <h4>This is an experimental annotation. As such, it is unsupported; we do not make any guarantees that it will work properly, and you use it at your own risk.</h4>
*/
public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
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@ -84,7 +84,8 @@ import java.io.PrintStream;
* <p/>
* <h3>Examples</h3>
* <pre>
* -T CallableLociWalker \
* java -jar GenomeAnalysisTK.jar \
* -T CallableLoci \
* -I my.bam \
* -summary my.summary \
* -o my.bed

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
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@ -102,7 +102,7 @@ import java.util.*;
* <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T Coverage \
* -T DepthOfCoverage \
* -o file_name_base \
* -I input_bams.list
* [-geneList refSeq.sorted.txt] \

1
public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
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@ -46,6 +46,7 @@ public class DeprecatedToolChecks {
deprecatedGATKWalkers.put("TableRecalibration", "2.0 (use PrintReads with -BQSR instead; see documentation for usage)");
deprecatedGATKWalkers.put("AlignmentWalker", "2.2 (no replacement)");
deprecatedGATKWalkers.put("CountBestAlignments", "2.2 (no replacement)");
deprecatedGATKWalkers.put("SomaticIndelDetector", "2.0 (replaced by the standalone tool Indelocator; see Cancer Tools documentation)");
}
// Mapping from walker name to major version number where the walker first disappeared and optional replacement options

32
public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
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@ -1,6 +1,6 @@
/*
* Copyright (c) 2012 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
@ -9,10 +9,10 @@
* 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
@ -37,6 +37,8 @@ import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.collections.Pair;
@ -295,6 +297,8 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
// Get annotation info (what type of annotation, standard etc.)
final HashSet<String> annotInfo = getAnnotInfo(myClass, new HashSet<String>());
root.put("annotinfo", StringUtils.join(annotInfo, ", "));
// Get annotation field (whether it goes in INFO or FORMAT)
root.put("annotfield", getAnnotField(myClass));
// Get walker type if applicable
root.put("walkertype", getWalkerType(myClass));
// Get partition type if applicable
@ -316,6 +320,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
// put empty items to avoid blowups
root.put("parallel", new HashSet<String>());
root.put("annotinfo", "");
root.put("annotfield", "");
root.put("walkertype", "");
root.put("partitiontype", "");
root.put("readfilters", new HashSet<HashMap<String, Object>>());
@ -359,6 +364,27 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
return getParallelism(mySuperClass, parallelOptions);
}
/**
* Utility function that looks up whether the annotation goes in INFO or FORMAT field.
*
* @param myClass the class to query for the interfaces
* @return a String specifying the annotation field
*/
private final String getAnnotField(Class myClass) {
//
// Look up superclasses recursively until we find either
// GenotypeAnnotation or InfoFieldAnnotation
final Class mySuperClass = myClass.getSuperclass();
if (mySuperClass == InfoFieldAnnotation.class) {
return "INFO (variant-level)";
} else if (mySuperClass == GenotypeAnnotation.class) {
return "FORMAT (sample genotype-level)";
} else if (mySuperClass.getSimpleName().equals("Object")) {
return "";
}
return getAnnotField(mySuperClass);
}
/**
* Utility function that determines the annotation type for an instance of class c.
*

7
settings/helpTemplates/generic.template.html
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@ -123,8 +123,13 @@
<small>${partitiontype}</small>
</h3>
</#if>
<#if annotfield != "" >
<h3>VCF Field
<small>${annotfield}</small>
</h3>
</#if>
<#if annotinfo != "" >
<h3>Annotation type
<h3>Type
<small>${annotinfo}</small>
</h3>
</#if>