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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2011-08-18 10:58:04 -04:00
parent bb79d3edae c2287c93d7
commit c08a9964d4
38 changed files with 353 additions and 351 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -34,10 +34,7 @@ import org.broadinstitute.sting.gatk.filters.ReadFilter;
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.GATKDoclet;
import org.broadinstitute.sting.utils.help.*;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*;
@ -178,7 +175,7 @@ public class CommandLineGATK extends CommandLineExecutable {
Formatter formatter = new Formatter(additionalHelp);
formatter.format("For a full description of this walker, see its GATKdocs at:%n");
formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType));
formatter.format("%s%n", HelpUtils.helpLinksToGATKDocs(walkerType));
return additionalHelp.toString();
}

72
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -1,10 +1,11 @@
package org.broadinstitute.sting.gatk.refdata;
import net.sf.samtools.util.SequenceUtil;
import org.broad.tribble.Feature;
import org.broad.tribble.annotation.Strand;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broad.tribble.gelitext.GeliTextFeature;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
@ -92,6 +93,67 @@ public class VariantContextAdaptors {
// --------------------------------------------------------------------------------------------------------------
private static class DBSnpAdaptor implements VCAdaptor {
private static boolean isSNP(DbSNPFeature feature) {
return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
}
private static boolean isMNP(DbSNPFeature feature) {
return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
}
private static boolean isInsertion(DbSNPFeature feature) {
return feature.getVariantType().contains("insertion");
}
private static boolean isDeletion(DbSNPFeature feature) {
return feature.getVariantType().contains("deletion");
}
private static boolean isIndel(DbSNPFeature feature) {
return isInsertion(feature) || isDeletion(feature) || isComplexIndel(feature);
}
public static boolean isComplexIndel(DbSNPFeature feature) {
return feature.getVariantType().contains("in-del");
}
/**
* gets the alternate alleles. This method should return all the alleles present at the location,
* NOT including the reference base. This is returned as a string list with no guarantee ordering
* of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
* frequency).
*
* @return an alternate allele list
*/
public static List<String> getAlternateAlleleList(DbSNPFeature feature) {
List<String> ret = new ArrayList<String>();
for (String allele : getAlleleList(feature))
if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele);
return ret;
}
/**
* gets the alleles. This method should return all the alleles present at the location,
* including the reference base. The first allele should always be the reference allele, followed
* by an unordered list of alternate alleles.
*
* @return an alternate allele list
*/
public static List<String> getAlleleList(DbSNPFeature feature) {
List<String> alleleList = new ArrayList<String>();
// add ref first
if ( feature.getStrand() == Strand.POSITIVE )
alleleList = Arrays.asList(feature.getObserved());
else
for (String str : feature.getObserved())
alleleList.add(SequenceUtil.reverseComplement(str));
if ( alleleList.size() > 0 && alleleList.contains(feature.getNCBIRefBase())
&& !alleleList.get(0).equals(feature.getNCBIRefBase()) )
Collections.swap(alleleList, alleleList.indexOf(feature.getNCBIRefBase()), 0);
return alleleList;
}
/**
* Converts non-VCF formatted dbSNP records to VariantContext.
* @return DbSNPFeature.
@ -102,18 +164,18 @@ public class VariantContextAdaptors {
@Override
public VariantContext convert(String name, Object input, ReferenceContext ref) {
DbSNPFeature dbsnp = (DbSNPFeature)input;
if ( ! Allele.acceptableAlleleBases(DbSNPHelper.getReference(dbsnp)) )
if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) )
return null;
Allele refAllele = Allele.create(DbSNPHelper.getReference(dbsnp), true);
Allele refAllele = Allele.create(dbsnp.getNCBIRefBase(), true);
if ( DbSNPHelper.isSNP(dbsnp) || DbSNPHelper.isIndel(dbsnp) || DbSNPHelper.isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) {
if ( isSNP(dbsnp) || isIndel(dbsnp) || isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) {
// add the reference allele
List<Allele> alleles = new ArrayList<Allele>();
alleles.add(refAllele);
// add all of the alt alleles
boolean sawNullAllele = refAllele.isNull();
for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) {
for ( String alt : getAlternateAlleleList(dbsnp) ) {
if ( ! Allele.acceptableAlleleBases(alt) ) {
//System.out.printf("Excluding dbsnp record %s%n", dbsnp);
return null;

169
public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java
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@ -1,169 +0,0 @@
/*
* 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.refdata.features;
import net.sf.samtools.util.SequenceUtil;
import org.broad.tribble.annotation.Strand;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
/**
* this class contains static helper methods for DbSNP
*/
public class DbSNPHelper {
private DbSNPHelper() {} // don't make a DbSNPHelper
public static String rsIDOfFirstRealVariant(List<VariantContext> VCs, VariantContext.Type type) {
if ( VCs == null )
return null;
String rsID = null;
for ( VariantContext vc : VCs ) {
if ( vc.getType() == type ) {
rsID = vc.getID();
break;
}
}
return rsID;
}
/**
* get the -1 * (log 10 of the error value)
*
* @return the log based error estimate
*/
public static double getNegLog10PError(DbSNPFeature feature) {
return 4; // -log10(0.0001)
}
//
// What kind of variant are we?
//
// ----------------------------------------------------------------------
public static boolean isSNP(DbSNPFeature feature) {
return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
}
public static boolean isMNP(DbSNPFeature feature) {
return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
}
public static String toMediumString(DbSNPFeature feature) {
String s = String.format("%s:%d:%s:%s", feature.getChr(), feature.getStart(), feature.getRsID(), Utils.join("",feature.getObserved()));
if (isSNP(feature)) s += ":SNP";
if (isIndel(feature)) s += ":Indel";
if (isHapmap(feature)) s += ":Hapmap";
if (is2Hit2Allele(feature)) s += ":2Hit";
return s;
}
public static boolean isInsertion(DbSNPFeature feature) {
return feature.getVariantType().contains("insertion");
}
public static boolean isDeletion(DbSNPFeature feature) {
return feature.getVariantType().contains("deletion");
}
public static boolean isIndel(DbSNPFeature feature) {
return DbSNPHelper.isInsertion(feature) || DbSNPHelper.isDeletion(feature) || DbSNPHelper.isComplexIndel(feature);
}
public static boolean isComplexIndel(DbSNPFeature feature) {
return feature.getVariantType().contains("in-del");
}
public static boolean isHapmap(DbSNPFeature feature) {
return feature.getValidationStatus().contains("by-hapmap");
}
public static boolean is2Hit2Allele(DbSNPFeature feature) {
return feature.getValidationStatus().contains("by-2hit-2allele");
}
public static boolean is1000genomes(DbSNPFeature feature) {
return feature.getValidationStatus().contains("by-1000genomes");
}
public static boolean isMQ1(DbSNPFeature feature) {
return feature.getWeight() == 1;
}
/**
* gets the alternate alleles. This method should return all the alleles present at the location,
* NOT including the reference base. This is returned as a string list with no guarantee ordering
* of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
* frequency).
*
* @return an alternate allele list
*/
public static List<String> getAlternateAlleleList(DbSNPFeature feature) {
List<String> ret = new ArrayList<String>();
for (String allele : getAlleleList(feature))
if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele);
return ret;
}
public static boolean onFwdStrand(DbSNPFeature feature) {
return feature.getStrand() == Strand.POSITIVE;
}
public static String getReference(DbSNPFeature feature) {
return feature.getNCBIRefBase();
}
public static String toSimpleString(DbSNPFeature feature) {
return String.format("%s:%s:%s", feature.getRsID(), feature.getObserved(), (feature.getStrand() == Strand.POSITIVE) ? "+" : "-");
}
/**
* gets the alleles. This method should return all the alleles present at the location,
* including the reference base. The first allele should always be the reference allele, followed
* by an unordered list of alternate alleles.
*
* @return an alternate allele list
*/
public static List<String> getAlleleList(DbSNPFeature feature) {
List<String> alleleList = new ArrayList<String>();
// add ref first
if ( onFwdStrand(feature) )
alleleList = Arrays.asList(feature.getObserved());
else
for (String str : feature.getObserved())
alleleList.add(SequenceUtil.reverseComplement(str));
if ( alleleList.size() > 0 && alleleList.contains(getReference(feature)) && !alleleList.get(0).equals(getReference(feature)) )
Collections.swap(alleleList, alleleList.indexOf(getReference(feature)), 0);
return alleleList;
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -26,7 +26,6 @@
package org.broadinstitute.sting.gatk.walkers;
import org.broad.tribble.Feature;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
@ -34,9 +33,6 @@ import org.broadinstitute.sting.commandline.RodBinding;
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.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -29,15 +29,11 @@ import org.broadinstitute.sting.commandline.RodBinding;
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.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationInterfaceManager;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -158,7 +154,7 @@ public class VariantAnnotatorEngine {
private void annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map<String, Object> infoAnnotations) {
for ( Map.Entry<RodBinding<VariantContext>, String> dbSet : dbAnnotations.entrySet() ) {
if ( dbSet.getValue().equals(VCFConstants.DBSNP_KEY) ) {
String rsID = DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
String rsID = VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
infoAnnotations.put(VCFConstants.DBSNP_KEY, rsID != null);
// annotate dbsnp id if available and not already there
if ( rsID != null && (!vc.hasID() || vc.getID().equals(VCFConstants.EMPTY_ID_FIELD)) )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;

185
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
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@ -42,50 +42,190 @@ import java.io.PrintStream;
/**
* Emits a data file containing information about callable, uncallable, poorly mapped, and other parts of the genome
*
* @Author depristo
* @Date May 7, 2010
* <p>
* A very common question about a NGS set of reads is what areas of the genome are considered callable. The system
* considers the coverage at each locus and emits either a per base state or a summary interval BED file that
* partitions the genomic intervals into the following callable states:
* <dl>
* <dt>REF_N</dt>
* <dd>the reference base was an N, which is not considered callable the GATK</dd>
* <dt>CALLABLE</dt>
* <dd>the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE</dd>
* <dt>NO_COVERAGE</dt>
* <dd>absolutely no reads were seen at this locus, regardless of the filtering parameters</dd>
* <dt>LOW_COVERAGE</dt>
* <dd>there were less than min. depth bases at the locus, after applying filters</dd>
* <dt>EXCESSIVE_COVERAGE</dt>
* <dd>more than -maxDepth read at the locus, indicating some sort of mapping problem</dd>
* <dt>POOR_MAPPING_QUALITY</dt>
* <dd>more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads</dd>
* </dl>
* </p>
*
* <h2>Input</h2>
* <p>
* A BAM file containing <b>exactly one sample</b>.
* </p>
*
* <h2>Output</h2>
* <p>
* <ul>
* <li>-o: a OutputFormatted (recommended BED) file with the callable status covering each base</li>
* <li>-summary: a table of callable status x count of all examined bases</li>
* </ul>
* </p>
*
* <h2>Examples</h2>
* <pre>
* -T CallableLociWalker \
* -I my.bam \
* -summary my.summary \
* -o my.bed
* </pre>
*
* would produce a BED file (my.bed) that looks like:
*
* <pre>
* 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...
* </pre>
* as well as a summary table that looks like:
*
* <pre>
* state nBases
* REF_N 0
* CALLABLE 996046
* NO_COVERAGE 121
* LOW_COVERAGE 928
* EXCESSIVE_COVERAGE 0
* POOR_MAPPING_QUALITY 2906
* </pre>
*
* @author Mark DePristo
* @since May 7, 2010
*/
@By(DataSource.REFERENCE)
public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableBaseState, CallableLociWalker.Integrator> {
@Output
PrintStream out;
@Argument(fullName = "maxLowMAPQ", shortName = "mlmq", doc = "Maximum value for MAPQ to be considered a problematic mapped read. The gap between this value and mmq are reads that are not sufficiently well mapped for calling but aren't indicative of mapping problems.", required = false)
/**
* Callable loci summary counts (see outputs) will be written to this file.
*/
@Output(fullName = "summary", shortName = "summary", doc = "Name of file for output summary", required = true)
File summaryFile;
/**
* The gap between this value and mmq are reads that are not sufficiently well mapped for calling but
* aren't indicative of mapping problems. For example, if maxLowMAPQ = 1 and mmq = 20, then reads with
* MAPQ == 0 are poorly mapped, MAPQ >= 20 are considered as contributing to calling, where
* reads with MAPQ >= 1 and < 20 are not bad in and of themselves but aren't sufficiently good to contribute to
* calling. In effect this reads are invisible, driving the base to the NO_ or LOW_COVERAGE states
*/
@Argument(fullName = "maxLowMAPQ", shortName = "mlmq", doc = "Maximum value for MAPQ to be considered a problematic mapped read.", required = false)
byte maxLowMAPQ = 1;
@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to 50.", required = false)
/**
* Reads with MAPQ > minMappingQuality are treated as usable for variation detection, contributing to the CALLABLE
* state.
*/
@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth.", required = false)
byte minMappingQuality = 10;
@Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth. Defaults to 20.", required = false)
/**
* Bases with less than minBaseQuality are viewed as not sufficiently high quality to contribute to the CALLABLE state
*/
@Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth.", required = false)
byte minBaseQuality = 20;
/**
* If the number of QC+ bases (on reads with MAPQ > minMappingQuality and with base quality > minBaseQuality) exceeds this
* value and is less than maxDepth the site is considered CALLABLE.
*/
@Argument(fullName = "minDepth", shortName = "minDepth", doc = "Minimum QC+ read depth before a locus is considered callable", required = false)
int minDepth = 4;
/**
* If the QC+ depth exceeds this value the site is considered to have EXCESSIVE_DEPTH
*/
@Argument(fullName = "maxDepth", shortName = "maxDepth", doc = "Maximum read depth before a locus is considered poorly mapped", required = false)
int maxDepth = -1;
/**
* We don't want to consider a site as POOR_MAPPING_QUALITY just because it has two reads, and one is MAPQ. We
* won't assign a site to the POOR_MAPPING_QUALITY state unless there are at least minDepthForLowMAPQ reads
* covering the site.
*/
@Argument(fullName = "minDepthForLowMAPQ", shortName = "mdflmq", doc = "Minimum read depth before a locus is considered a potential candidate for poorly mapped", required = false)
int minDepthLowMAPQ = 10;
@Argument(fullName = "maxFractionOfReadsWithLowMAPQ", shortName = "frlmq", doc = "Maximum read depth before a locus is considered poorly mapped", required = false)
/**
* If the number of reads at this site is greater than minDepthForLowMAPQ and the fraction of reads with low mapping quality
* exceeds this fraction then the site has POOR_MAPPING_QUALITY.
*/
@Argument(fullName = "maxFractionOfReadsWithLowMAPQ", shortName = "frlmq", doc = "If the fraction of reads at a base with low mapping quality exceeds this value, the site may be poorly mapped", required = false)
double maxLowMAPQFraction = 0.1;
@Argument(fullName = "format", shortName = "format", doc = "Output format for the system: either BED or STATE_PER_BASE", required = false)
/**
* The output of this walker will be written in this format. The recommended option is BED.
*/
@Argument(fullName = "format", shortName = "format", doc = "Output format", required = false)
OutputFormat outputFormat;
@Argument(fullName = "summary", shortName = "summary", doc = "Name of file for output summary", required = true)
File summaryFile;
public enum OutputFormat {
/**
* The output will be written as a BED file. There's a BED element for each
* continuous run of callable states (i.e., CALLABLE, REF_N, etc). This is the recommended
* format
*/
BED,
public enum OutputFormat { BED, STATE_PER_BASE }
/**
* Emit chr start stop state quads for each base. Produces a potentially disasterously
* large amount of output.
*/
STATE_PER_BASE
}
public enum CalledState {
/** the reference base was an N, which is not considered callable the GATK */
REF_N,
/** the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE */
CALLABLE,
/** absolutely no reads were seen at this locus, regardless of the filtering parameters */
NO_COVERAGE,
/** there were less than min. depth bases at the locus, after applying filters */
LOW_COVERAGE,
/** more than -maxDepth read at the locus, indicating some sort of mapping problem */
EXCESSIVE_COVERAGE,
/** more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads */
POOR_MAPPING_QUALITY
}
////////////////////////////////////////////////////////////////////////////////////
// STANDARD WALKER METHODS
////////////////////////////////////////////////////////////////////////////////////
@Override
public boolean includeReadsWithDeletionAtLoci() { return true; }
@Override
public void initialize() {
if ( getToolkit().getSamples().size() > 1 )
throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getToolkit().getSamples());
try {
PrintStream summaryOut = new PrintStream(summaryFile);
summaryOut.close();
@ -94,15 +234,15 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
}
}
public static class Integrator {
long counts[] = new long[CalledState.values().length];
protected static class Integrator {
final long counts[] = new long[CalledState.values().length];
CallableBaseState state = null;
}
public static class CallableBaseState implements HasGenomeLocation {
public GenomeLocParser genomeLocParser;
protected static class CallableBaseState implements HasGenomeLocation {
final public GenomeLocParser genomeLocParser;
public GenomeLoc loc;
public CalledState state;
final public CalledState state;
public CallableBaseState(GenomeLocParser genomeLocParser,GenomeLoc loc, CalledState state) {
this.genomeLocParser = genomeLocParser;
@ -133,16 +273,10 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
public String toString() {
return String.format("%s %d %d %s", loc.getContig(), loc.getStart(), loc.getStop(), state);
//return String.format("%s %d %d %d %s", loc.getContig(), loc.getStart(), loc.getStop(), loc.getStop() - loc.getStart() + 1, state);
}
}
public enum CalledState { REF_N, CALLABLE, NO_COVERAGE, LOW_COVERAGE, EXCESSIVE_COVERAGE, POOR_MAPPING_QUALITY }
public Integrator reduceInit() {
return new Integrator();
}
@Override
public CallableBaseState map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
CalledState state;
@ -179,6 +313,12 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
return new CallableBaseState(getToolkit().getGenomeLocParser(),context.getLocation(), state);
}
@Override
public Integrator reduceInit() {
return new Integrator();
}
@Override
public Integrator reduce(CallableBaseState state, Integrator integrator) {
// update counts
integrator.counts[state.getState().ordinal()]++;
@ -206,6 +346,7 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
// INTERVAL ON TRAVERSAL DONE
////////////////////////////////////////////////////////////////////////////////////
@Override
public void onTraversalDone(Integrator result) {
// print out the last state
if ( result != null ) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
View File

@ -32,8 +32,8 @@ 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.refdata.SeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
View File

@ -39,9 +39,9 @@ import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.features.refseq.Transcript;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
import org.broadinstitute.sting.utils.codecs.refseq.Transcript;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
View File

@ -32,7 +32,7 @@ import org.broadinstitute.sting.commandline.RodBinding;
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.refdata.features.sampileup.SAMPileupFeature;
import org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
View File

@ -14,9 +14,8 @@ import org.broadinstitute.sting.commandline.RodBinding;
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.refdata.features.table.TableFeature;
import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.BaseUtils;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -33,7 +33,6 @@ 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.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*;
@ -120,7 +119,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )
return 0;
String rsID = dbsnp == null ? null : DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP);
String rsID = dbsnp == null ? null : VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP);
Collection<VariantContext> contexts = getVariantContexts(tracker, ref);

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.features.beagle;
package org.broadinstitute.sting.utils.codecs.beagle;
/*
* Copyright (c) 2010 The Broad Institute
*

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java
View File

@ -22,7 +22,7 @@
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features.beagle;
package org.broadinstitute.sting.utils.codecs.beagle;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.variantcontext.Allele;

2
public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
View File

@ -117,7 +117,7 @@ public class CGVarCodec implements FeatureCodec {
return new VariantContext("CGI", array[3], start, end, alleles, VariantContext.NO_NEG_LOG_10PERROR, null, attrs);
}
public Class getFeatureType() {
public Class<VariantContext> getFeatureType() {
return VariantContext.class;
}

2
public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
View File

@ -82,7 +82,7 @@ public class RawHapMapCodec implements FeatureCodec {
headerLine);
}
public Class getFeatureType() {
public Class<RawHapMapFeature> getFeatureType() {
return RawHapMapFeature.class;
}

5
public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
View File

@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.refdata.features.refseq;
package org.broadinstitute.sting.utils.codecs.refseq;
import org.apache.commons.io.filefilter.FalseFileFilter;
import org.broad.tribble.Feature;
import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.LineReader;
@ -104,7 +103,7 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
}
@Override
public Class getFeatureType() {
public Class<RefSeqFeature> getFeatureType() {
return RefSeqFeature.class;
}
}

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.features.refseq;
package org.broadinstitute.sting.utils.codecs.refseq;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;

106
public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/Transcript.java → public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java
View File

@ -1,53 +1,53 @@
package org.broadinstitute.sting.gatk.refdata.features.refseq;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: asivache
* Date: Sep 22, 2009
* Time: 5:22:30 PM
* To change this template use File | Settings | File Templates.
*/
public interface Transcript extends HasGenomeLocation {
/** Returns id of the transcript (RefSeq NM_* id) */
public String getTranscriptId();
/** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
public int getStrand();
/** Returns transcript's full genomic interval (includes all exons with UTRs) */
public GenomeLoc getLocation();
/** Returns genomic interval of the coding sequence (does not include
* UTRs, but still includes introns, since it's a single interval on the DNA)
*/
public GenomeLoc getCodingLocation();
/** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc,
* but the implementation can decide otherwise)
*/
public String getGeneName();
/** Number of exons in this transcript */
public int getNumExons();
/** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */
public GenomeLoc getExonLocation(int n);
/** Returns the list of all exons in this transcript, as genomic intervals */
public List<GenomeLoc> getExons();
/** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
public boolean overlapsP (GenomeLoc that);
/** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
* NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
* but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
* @see #overlapsExonP
*/
public boolean overlapsCodingP (GenomeLoc that);
/** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
public boolean overlapsExonP (GenomeLoc that);
}
package org.broadinstitute.sting.utils.codecs.refseq;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: asivache
* Date: Sep 22, 2009
* Time: 5:22:30 PM
* To change this template use File | Settings | File Templates.
*/
public interface Transcript extends HasGenomeLocation {
/** Returns id of the transcript (RefSeq NM_* id) */
public String getTranscriptId();
/** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
public int getStrand();
/** Returns transcript's full genomic interval (includes all exons with UTRs) */
public GenomeLoc getLocation();
/** Returns genomic interval of the coding sequence (does not include
* UTRs, but still includes introns, since it's a single interval on the DNA)
*/
public GenomeLoc getCodingLocation();
/** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc,
* but the implementation can decide otherwise)
*/
public String getGeneName();
/** Number of exons in this transcript */
public int getNumExons();
/** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */
public GenomeLoc getExonLocation(int n);
/** Returns the list of all exons in this transcript, as genomic intervals */
public List<GenomeLoc> getExons();
/** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
public boolean overlapsP (GenomeLoc that);
/** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
* NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
* but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
* @see #overlapsExonP
*/
public boolean overlapsCodingP (GenomeLoc that);
/** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
public boolean overlapsExonP (GenomeLoc that);
}

4
public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features.sampileup;
package org.broadinstitute.sting.utils.codecs.sampileup;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
@ -35,7 +35,7 @@ import java.util.ArrayList;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import static org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature.VariantType;
import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.VariantType;
/**
* A Tribble encoder / decoder for SAM pileup data.

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features.sampileup;
package org.broadinstitute.sting.utils.codecs.sampileup;
import net.sf.samtools.util.StringUtil;
import org.broad.tribble.Feature;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
View File

@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features.samread;
package org.broadinstitute.sting.utils.codecs.samread;
import net.sf.samtools.Cigar;
import net.sf.samtools.TextCigarCodec;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java
View File

@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.features.samread;
package org.broadinstitute.sting.utils.codecs.samread;
import org.broad.tribble.Feature;

2
public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java
View File

@ -222,7 +222,7 @@ public class SnpEffCodec implements FeatureCodec, SelfScopingFeatureCodec {
return null;
}
public Class getFeatureType() {
public Class<SnpEffFeature> getFeatureType() {
return SnpEffFeature.class;
}

2
public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
View File

@ -178,7 +178,7 @@ public class SoapSNPCodec implements FeatureCodec, NameAwareCodec {
/**
* @return VariantContext
*/
public Class getFeatureType() {
public Class<VariantContext> getFeatureType() {
return VariantContext.class;
}

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.features.table;
package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;

4
public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.features.table;
package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broad.tribble.readers.LineReader;
@ -51,7 +51,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
}
@Override
public Class getFeatureType() {
public Class<TableFeature> getFeatureType() {
return TableFeature.class;
}

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.features.table;
package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.GenomeLoc;

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
View File

@ -263,7 +263,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
*
* @return the type of record
*/
public Class getFeatureType() {
public Class<VariantContext> getFeatureType() {
return VariantContext.class;
}

15
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
View File

@ -180,4 +180,19 @@ public class VCFUtils {
return new HashSet<VCFHeaderLine>(map.values());
}
public static String rsIDOfFirstRealVariant(List<VariantContext> VCs, VariantContext.Type type) {
if ( VCs == null )
return null;
String rsID = null;
for ( VariantContext vc : VCs ) {
if ( vc.getType() == type ) {
rsID = vc.getID();
break;
}
}
return rsID;
}
}

2
public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
View File

@ -71,7 +71,7 @@ public abstract class DocumentedGATKFeatureHandler {
* @return
*/
public String getDestinationFilename(ClassDoc doc, Class clazz) {
return GATKDocUtils.htmlFilenameForClass(clazz);
return HelpUtils.htmlFilenameForClass(clazz);
}
/**

48
public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
View File

@ -1,48 +0,0 @@
/*
* 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;
/**
* @author depristo
* @since 8/8/11
*/
public class GATKDocUtils {
private final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
private final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
private final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
public static String htmlFilenameForClass(Class c) {
return c.getName().replace(".", "_") + ".html";
}
public static String helpLinksToGATKDocs(Class c) {
String classPath = htmlFilenameForClass(c);
StringBuilder b = new StringBuilder();
b.append("release version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n");
b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
return b.toString();
}
}

17
public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
View File

@ -32,6 +32,10 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
import java.lang.reflect.Field;
public class HelpUtils {
public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
protected static boolean implementsInterface(ProgramElementDoc classDoc, Class... interfaceClasses) {
for (Class interfaceClass : interfaceClasses)
if (assignableToClass(classDoc, interfaceClass, false))
@ -74,4 +78,17 @@ public class HelpUtils {
String.format("%s.%s", containingPackage.name(), doc.name()) :
String.format("%s", doc.name());
}
public static String htmlFilenameForClass(Class c) {
return c.getName().replace(".", "_") + ".html";
}
public static String helpLinksToGATKDocs(Class c) {
String classPath = htmlFilenameForClass(c);
StringBuilder b = new StringBuilder();
b.append("release version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n");
b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
return b.toString();
}
}

2
public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
View File

@ -26,7 +26,6 @@
package org.broadinstitute.sting.commandline;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.testng.Assert;
@ -35,7 +34,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import javax.script.Bindings;
import java.util.List;
import java.util.EnumSet;
/**

2
public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
View File

@ -10,7 +10,7 @@ import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;

2
public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;

2
public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
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@ -31,7 +31,7 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GenomeLoc;

4
public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
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@ -29,8 +29,8 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.refdata.features.table.BedTableCodec;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.utils.codecs.table.BedTableCodec;
import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;