diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
index bdd41f37c..ae0b4a347 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
@@ -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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java
index 41ab59845..e576666e1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java
@@ -32,10 +32,23 @@ import org.broadinstitute.sting.commandline.Argument;
* A read filter (transformer) that sets all reads mapping quality to a given value.
*
*
- * 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).
*
*
+ * See also
+ *
+ * ReassignOneMappingQualityFilter: reassigns a single MAPQ value, as opposed to all those found in the BAM file.
+ *
+ * Caveats
+ *
+ * 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.
+ *
*
* Input
*
@@ -50,9 +63,9 @@ import org.broadinstitute.sting.commandline.Argument;
*
*
Examples
*
- * java
- * -jar GenomeAnalysisTK.jar
- * -rf ReassignMappingQuality
+ * java -jar GenomeAnalysisTK.jar \
+ * -T PrintReads \
+ * -rf ReassignMappingQuality \
* -DMQ 35
*
*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java
index f31313a86..232b7ed3d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java
@@ -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.
*
*
- * 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.
*
*
- *
* Input
*
* BAM file(s)
@@ -60,8 +59,8 @@ import org.broadinstitute.sting.commandline.Argument;
*
*
Examples
*
- * java
- * -jar GenomeAnalysisTK.jar
+ * java -jar GenomeAnalysisTK.jar
+ * -T PrintReads
* -rf ReassignOneMappingQuality
* -RMQF 255
* -RMQT 60
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index 6e7bc9805..87323cf87 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -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
+ *
+ * The allele balance is the fraction of ref bases over ref + alt bases.
+ *
+ * Caveats
+ * Note that this annotation will only work properly for biallelic samples that are called as heterozygous.
*/
public class AlleleBalance extends InfoFieldAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
index 608257b54..f5930078f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
@@ -51,7 +51,7 @@ import java.util.List;
* The allele balance is the fraction of ref bases over ref + alt bases.
*
* Caveats
- * Note that this annotation will only work properly for biallelic het-called samples.
+ * Note that this annotation will only work properly for biallelic samples that are called as heterozygous.
* 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.
*/
public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
index 6af6723f2..e30965925 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
@@ -84,7 +84,8 @@ import java.io.PrintStream;
*
* Examples
*
- * -T CallableLociWalker \
+ * java -jar GenomeAnalysisTK.jar \
+ * -T CallableLoci \
* -I my.bam \
* -summary my.summary \
* -o my.bed
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
index c4ef4d23b..ca3255097 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
@@ -102,7 +102,7 @@ import java.util.*;
*
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
- * -T Coverage \
+ * -T DepthOfCoverage \
* -o file_name_base \
* -I input_bams.list
* [-geneList refSeq.sorted.txt] \
diff --git a/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java b/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
index 78c32ed02..9823e524a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
+++ b/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
@@ -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
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index 02c269495..01221cf27 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -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 annotInfo = getAnnotInfo(myClass, new HashSet());
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());
root.put("annotinfo", "");
+ root.put("annotfield", "");
root.put("walkertype", "");
root.put("partitiontype", "");
root.put("readfilters", new HashSet>());
@@ -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.
*
diff --git a/settings/helpTemplates/generic.template.html b/settings/helpTemplates/generic.template.html
index b05ad65c0..ea9fa2d72 100644
--- a/settings/helpTemplates/generic.template.html
+++ b/settings/helpTemplates/generic.template.html
@@ -123,8 +123,13 @@
${partitiontype}
+ <#if annotfield != "" >
+ VCF Field
+ ${annotfield}
+
+
<#if annotinfo != "" >
- Annotation type
+ Type
${annotinfo}