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Resolving merge conflicts from VCF move

This commit is contained in:
Eric Banks 2013-01-06 14:32:31 -05:00
parent ef638489d5 8822b8e7c8
commit 0249e1f497
9 changed files with 95 additions and 26 deletions
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4
public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
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@ -32,8 +32,8 @@ import org.apache.log4j.PatternLayout;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.help.HelpFormatter;
import org.broadinstitute.sting.utils.help.HelpUtils;
import java.io.IOException;
import java.util.*;
@ -289,7 +289,7 @@ public abstract class CommandLineProgram {
*/
private static void printDocumentationReference() {
errorPrintf("Visit our website and forum for extensive documentation and answers to %n");
errorPrintf("commonly asked questions " + HelpUtils.BASE_GATK_URL + "%n");
errorPrintf("commonly asked questions " + HelpConstants.BASE_GATK_URL + "%n");
}

7
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -36,10 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.gatk.walkers.Attribution;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.GATKDocUtils;
import org.broadinstitute.sting.utils.help.HelpUtils;
import org.broadinstitute.sting.utils.help.*;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*;
@ -161,7 +158,7 @@ public class CommandLineGATK extends CommandLineExecutable {
List<String> header = new ArrayList<String>();
header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime()));
header.add("Copyright (c) 2010 The Broad Institute");
header.add("For support and documentation go to " + HelpUtils.BASE_GATK_URL);
header.add("For support and documentation go to " + HelpConstants.BASE_GATK_URL);
return header;
}

4
public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
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@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.filters;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.help.GATKDocUtils;
import org.broadinstitute.sting.utils.help.HelpUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.util.Collection;
import java.util.List;
@ -71,7 +71,7 @@ public class FilterManager extends PluginManager<ReadFilter> {
return String.format("Read filter %s not found. Available read filters:%n%n%s%n%n%s",pluginName,
userFriendlyListofReadFilters(availableFilters),
"Please consult the GATK Documentation (" + HelpUtils.GATK_DOCS_URL + ") for more information.");
"Please consult the GATK Documentation (" + HelpConstants.GATK_DOCS_URL + ") for more information.");
}
private String userFriendlyListofReadFilters(List<Class<? extends ReadFilter>> filters) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -32,8 +32,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.HelpUtils;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.variant.variantcontext.Allele;
@ -81,7 +81,7 @@ public class VariantDataManager {
final double theSTD = standardDeviation(theMean, iii);
logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
if( Double.isNaN(theMean) ) {
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.forumPost("discussion/49/using-variant-annotator"));
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 " + HelpConstants.forumPost("discussion/49/using-variant-annotator"));
}
foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);

6
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
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@ -30,7 +30,7 @@ import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.variant.variantcontext.VariantContext;
@ -278,7 +278,7 @@ public class UserException extends ReviewedStingException {
public static class ReadMissingReadGroup extends MalformedBAM {
public ReadMissingReadGroup(SAMRecord read) {
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.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
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 " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
}
}
@ -354,7 +354,7 @@ public class UserException extends ReviewedStingException {
super(String.format("Lexicographically sorted human genome sequence detected in %s."
+ "\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."
+ "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files."
+ "\nYou can use the ReorderSam utility to fix this problem: " + HelpUtils.forumPost("discussion/58/companion-utilities-reordersam")
+ "\nYou can use the ReorderSam utility to fix this problem: " + HelpConstants.forumPost("discussion/58/companion-utilities-reordersam")
+ "\n %s contigs = %s",
name, name, ReadUtils.prettyPrintSequenceRecords(dict)));
}

4
public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java
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@ -50,7 +50,7 @@ public class ForumAPIUtils {
Gson gson = new Gson();
List<String> output = new ArrayList<String>();
String text = httpGet(HelpUtils.GATK_FORUM_API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
String text = httpGet(HelpConstants.GATK_FORUM_API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
APIQuery details = gson.fromJson(text, APIQuery.class);
ForumDiscussion[] discussions = details.Discussions;
@ -158,7 +158,7 @@ public class ForumAPIUtils {
Gson gson = new Gson();
String data = gson.toJson(post.getPostData());
httpPost(data, HelpUtils.GATK_FORUM_API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
httpPost(data, HelpConstants.GATK_FORUM_API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
}

2
public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
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@ -28,7 +28,7 @@ public class GATKDocUtils {
/**
* The URL root for RELEASED GATKDOC units
*/
public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpUtils.GATK_DOCS_URL;
public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpConstants.GATK_DOCS_URL;
/**
* The URL root for STABLE GATKDOC units
*/

81
public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java 100644
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@ -0,0 +1,81 @@
/*
* 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.utils.help;
import com.sun.javadoc.FieldDoc;
import com.sun.javadoc.PackageDoc;
import com.sun.javadoc.ProgramElementDoc;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import java.lang.reflect.Field;
public class HelpConstants {
public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk";
public final static String GATK_DOCS_URL = BASE_GATK_URL + "/gatkdocs/";
public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
public static String forumPost(String post) {
return GATK_FORUM_URL + post;
}
protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
try {
Class type = getClassForDoc(classDoc);
return lhsClass.isAssignableFrom(type) && (!requireConcrete || JVMUtils.isConcrete(type));
} catch (Throwable t) {
// Ignore errors.
return false;
}
}
protected static Class getClassForDoc(ProgramElementDoc doc) throws ClassNotFoundException {
return Class.forName(getClassName(doc));
}
protected static Field getFieldForFieldDoc(FieldDoc fieldDoc) {
try {
Class clazz = getClassForDoc(fieldDoc.containingClass());
return JVMUtils.findField(clazz, fieldDoc.name());
} catch (ClassNotFoundException e) {
throw new RuntimeException(e);
}
}
/**
* Reconstitute the class name from the given class JavaDoc object.
*
* @param doc the Javadoc model for the given class.
* @return The (string) class name of the given class.
*/
protected static String getClassName(ProgramElementDoc doc) {
PackageDoc containingPackage = doc.containingPackage();
return containingPackage.name().length() > 0 ?
String.format("%s.%s", containingPackage.name(), doc.name()) :
String.format("%s", doc.name());
}
}

9
public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
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@ -33,15 +33,6 @@ import java.lang.reflect.Field;
public class HelpUtils {
public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk";
public final static String GATK_DOCS_URL = BASE_GATK_URL + "/gatkdocs/";
public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
public static String forumPost(String post) {
return GATK_FORUM_URL + post;
}
protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
try {
Class type = getClassForDoc(classDoc);