Merged bug fix from Stable into Unstable
This commit is contained in:
Eric Banks
commit
a82ec7ad80
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.help.ApplicationDetails;
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import org.broadinstitute.sting.utils.help.HelpFormatter;
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import org.broadinstitute.sting.utils.help.HelpUtils;
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import java.io.IOException;
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import java.util.*;
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@ -288,7 +289,7 @@ public abstract class CommandLineProgram {
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*/
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private static void printDocumentationReference() {
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errorPrintf("Visit our website and forum for extensive documentation and answers to %n");
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errorPrintf("commonly asked questions http://www.broadinstitute.org/gatk%n");
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errorPrintf("commonly asked questions " + HelpUtils.BASE_GATK_URL + "%n");
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}
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@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.help.ApplicationDetails;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.help.GATKDocUtils;
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import org.broadinstitute.sting.utils.help.HelpUtils;
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import org.broadinstitute.sting.utils.text.TextFormattingUtils;
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import java.util.*;
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@ -160,7 +161,7 @@ public class CommandLineGATK extends CommandLineExecutable {
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List<String> header = new ArrayList<String>();
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header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime()));
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header.add("Copyright (c) 2010 The Broad Institute");
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header.add("For support and documentation go to http://www.broadinstitute.org/gatk");
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header.add("For support and documentation go to " + HelpUtils.BASE_GATK_URL);
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return header;
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}
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@ -25,11 +25,9 @@
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package org.broadinstitute.sting.gatk.filters;
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import com.google.common.base.Function;
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import com.google.common.collect.Collections2;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.sting.utils.help.GATKDocUtils;
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import org.broadinstitute.sting.utils.help.HelpUtils;
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import java.util.Collection;
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import java.util.List;
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@ -73,7 +71,7 @@ public class FilterManager extends PluginManager<ReadFilter> {
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return String.format("Read filter %s not found. Available read filters:%n%n%s%n%n%s",pluginName,
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userFriendlyListofReadFilters(availableFilters),
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"Please consult the GATK Documentation (http://www.broadinstitute.org/gatk/gatkdocs/) for more information.");
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"Please consult the GATK Documentation (" + HelpUtils.GATK_DOCS_URL + ") for more information.");
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}
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private String userFriendlyListofReadFilters(List<Class<? extends ReadFilter>> filters) {
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@ -282,7 +282,8 @@ public class DiffEngine {
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// now that we have a specific list of values we want to show, display them
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GATKReport report = new GATKReport();
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final String tableName = "differences";
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report.addTable(tableName, "Summarized differences between the master and test files. See http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information", 3);
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// TODO for Geraldine -- link needs to be updated below
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report.addTable(tableName, "Summarized differences between the master and test files. See [ask Geraldine to fix link to DiffEngine wiki] for more information", 3);
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final GATKReportTable table = report.getTable(tableName);
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table.addColumn("Difference");
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table.addColumn("NumberOfOccurrences");
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@ -138,7 +138,8 @@ public class DiffObjects extends RodWalker<Integer, Integer> {
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/**
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* Writes out a file of the DiffEngine format:
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*
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* http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
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* TODO for Geraldine -- link needs to be updated below (and also in SelectVariants and RefSeqCodec GATK docs)
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* http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
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*/
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@Output(doc="File to which results should be written",required=true)
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protected PrintStream out;
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@ -13,7 +13,7 @@ import java.util.Set;
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/**
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* Stratifies the eval RODs by user-supplied JEXL expressions
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*
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* See http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions for more details
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* See http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk for more details
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*/
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public class JexlExpression extends VariantStratifier implements StandardStratification {
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// needs to know the jexl expressions
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@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.help.HelpUtils;
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import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
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import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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@ -80,7 +81,7 @@ public class VariantDataManager {
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final double theSTD = standardDeviation(theMean, iii);
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logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
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if( Double.isNaN(theMean) ) {
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throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator");
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throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See " + HelpUtils.GATK_FORUM_URL + "discussion/49/using-variant-annotator");
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}
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foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);
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@ -51,8 +51,7 @@ import java.util.*;
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* The Variant Validation Assessor is a tool for vetting/assessing validation data (containing genotypes).
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* The tool produces a VCF that is annotated with information pertaining to plate quality control and by
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* default is soft-filtered by high no-call rate or low Hardy-Weinberg probability.
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* If you have .ped files, please first convert them to VCF format
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* (see http://www.broadinstitute.org/gsa/wiki/index.php/Converting_ped_to_vcf).
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* If you have .ped files, please first convert them to VCF format.
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*
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* <h2>Input</h2>
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* <p>
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@ -30,6 +30,7 @@ import net.sf.samtools.SAMSequenceDictionary;
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import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.help.HelpUtils;
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import org.broadinstitute.sting.utils.sam.ReadUtils;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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@ -267,7 +268,7 @@ public class UserException extends ReviewedStingException {
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public static class ReadMissingReadGroup extends MalformedBAM {
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public ReadMissingReadGroup(SAMRecord read) {
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super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem", read.getReadName()));
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super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use " + HelpUtils.GATK_FORUM_URL + "discussion/59/companion-utilities-replacereadgroups to fix this problem", read.getReadName()));
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}
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}
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@ -343,7 +344,7 @@ public class UserException extends ReviewedStingException {
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super(String.format("Lexicographically sorted human genome sequence detected in %s."
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+ "\nFor safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs."
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+ "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files."
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+ "\nYou can use the ReorderSam utility to fix this problem: http://www.broadinstitute.org/gsa/wiki/index.php/ReorderSam"
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+ "\nYou can use the ReorderSam utility to fix this problem: " + HelpUtils.GATK_FORUM_URL + "discussion/58/companion-utilities-reordersam"
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+ "\n %s contigs = %s",
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name, name, ReadUtils.prettyPrintSequenceRecords(dict)));
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}
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@ -44,14 +44,13 @@ public class ForumAPIUtils {
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/**
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* How we post to the forum
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*/
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private final static String API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
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final private static String ACCESS_TOKEN = "access_token=";
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public static List<String> getPostedTools(String forumKey) {
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Gson gson = new Gson();
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List<String> output = new ArrayList<String>();
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String text = httpGet(API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
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String text = httpGet(HelpUtils.GATK_FORUM_API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
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APIQuery details = gson.fromJson(text, APIQuery.class);
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ForumDiscussion[] discussions = details.Discussions;
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@ -159,7 +158,7 @@ public class ForumAPIUtils {
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Gson gson = new Gson();
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String data = gson.toJson(post.getPostData());
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httpPost(data, API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
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httpPost(data, HelpUtils.GATK_FORUM_API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
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}
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@ -167,8 +166,7 @@ public class ForumAPIUtils {
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class APIQuery {
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ForumDiscussion[] Discussions;
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public APIQuery() {
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}
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public APIQuery() {}
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}
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}
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@ -28,7 +28,7 @@ public class GATKDocUtils {
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/**
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* The URL root for RELEASED GATKDOC units
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*/
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public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gatk/gatkdocs/";
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public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpUtils.GATK_DOCS_URL;
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/**
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* The URL root for STABLE GATKDOC units
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*/
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@ -32,6 +32,15 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
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import java.lang.reflect.Field;
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public class HelpUtils {
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public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk";
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public final static String GATK_DOCS_URL = BASE_GATK_URL + "/gatkdocs/";
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public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
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public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
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protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
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try {
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Class type = getClassForDoc(classDoc);
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@ -71,7 +71,6 @@ abstract class SortingVariantContextWriterBase implements VariantContextWriter {
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this.takeOwnershipOfInner = takeOwnershipOfInner;
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// has to be PriorityBlockingQueue to be thread-safe
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// see http://getsatisfaction.com/gsa/topics/missing_loci_output_in_multi_thread_mode_when_implement_sortingvcfwriterbase?utm_content=topic_link&utm_medium=email&utm_source=new_topic
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this.queue = new PriorityBlockingQueue<VCFRecord>(50, new VariantContextComparator());
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this.mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC;
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@ -28,7 +28,6 @@ public class VCFIntegrationTest extends WalkerTest {
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}
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@Test(enabled = true)
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// See https://getsatisfaction.com/gsa/topics/support_vcf_4_1_structural_variation_breakend_alleles?utm_content=topic_link&utm_medium=email&utm_source=new_topic
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public void testReadingAndWritingBreakpointAlleles() {
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String testVCF = privateTestDir + "breakpoint-example.vcf";
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