Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Guillermo del Angel
commit
269ed1206c
|
|
@ -0,0 +1,40 @@
|
|||
/*
|
||||
* 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.commandline;
|
||||
|
||||
import java.lang.annotation.*;
|
||||
|
||||
/**
|
||||
* Indicates that a walker argument should is considered an advanced option.
|
||||
*
|
||||
* @author Mark DePristo
|
||||
* @version 0.1
|
||||
*/
|
||||
@Documented
|
||||
@Inherited
|
||||
@Retention(RetentionPolicy.RUNTIME)
|
||||
@Target({ElementType.TYPE,ElementType.FIELD})
|
||||
public @interface Advanced {
|
||||
}
|
||||
|
|
@ -151,6 +151,14 @@ public class ArgumentSource {
|
|||
return field.isAnnotationPresent(Hidden.class) || field.isAnnotationPresent(Deprecated.class);
|
||||
}
|
||||
|
||||
/**
|
||||
* Is the given argument considered an advanced option when displaying on the command-line argument system.
|
||||
* @return True if so. False otherwise.
|
||||
*/
|
||||
public boolean isAdvanced() {
|
||||
return field.isAnnotationPresent(Advanced.class);
|
||||
}
|
||||
|
||||
/**
|
||||
* Is this command-line argument dependent on some primitive argument types?
|
||||
* @return True if this command-line argument depends on other arguments; false otherwise.
|
||||
|
|
|
|||
|
|
@ -325,7 +325,7 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
|
|||
|
||||
@Override
|
||||
public Object createTypeDefault(ParsingEngine parsingEngine, ArgumentSource source, Type type) {
|
||||
Class parameterType = getParameterizedTypeClass(type);
|
||||
Class parameterType = JVMUtils.getParameterizedTypeClass(type);
|
||||
return RodBinding.makeUnbound((Class<? extends Feature>)parameterType);
|
||||
}
|
||||
|
||||
|
|
@ -338,6 +338,8 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
|
|||
public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches) {
|
||||
ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
|
||||
String value = getArgumentValue( defaultDefinition, matches );
|
||||
Class<? extends Feature> parameterType = JVMUtils.getParameterizedTypeClass(type);
|
||||
|
||||
try {
|
||||
String name = defaultDefinition.fullName;
|
||||
String tribbleType = null;
|
||||
|
|
@ -373,18 +375,18 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
|
|||
if ( featureDescriptor != null ) {
|
||||
tribbleType = featureDescriptor.getName();
|
||||
logger.warn("Dynamically determined type of " + file + " to be " + tribbleType);
|
||||
} else {
|
||||
throw new UserException.CommandLineException(
|
||||
String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +
|
||||
"Please add an explicit type tag :TYPE listing the correct type from among the supported types: %s",
|
||||
manager.userFriendlyListOfAvailableFeatures()));
|
||||
}
|
||||
}
|
||||
|
||||
if ( tribbleType == null )
|
||||
throw new UserException.CommandLineException(
|
||||
String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +
|
||||
"Please add an explicit type tag :NAME listing the correct type from among the supported types:%n%s",
|
||||
manager.userFriendlyListOfAvailableFeatures(parameterType)));
|
||||
}
|
||||
}
|
||||
|
||||
Constructor ctor = (makeRawTypeIfNecessary(type)).getConstructor(Class.class, String.class, String.class, String.class, Tags.class);
|
||||
Class parameterType = getParameterizedTypeClass(type);
|
||||
RodBinding result = (RodBinding)ctor.newInstance(parameterType, name, value, tribbleType, tags);
|
||||
parsingEngine.addTags(result,tags);
|
||||
parsingEngine.addRodBinding(result);
|
||||
|
|
@ -399,16 +401,6 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
|
|||
value, source.field.getName(), e.getMessage()));
|
||||
}
|
||||
}
|
||||
|
||||
private Class getParameterizedTypeClass(Type t) {
|
||||
if ( t instanceof ParameterizedType ) {
|
||||
ParameterizedType parameterizedType = (ParameterizedType)t;
|
||||
if ( parameterizedType.getActualTypeArguments().length != 1 )
|
||||
throw new ReviewedStingException("BUG: more than 1 generic type found on class" + t);
|
||||
return (Class)parameterizedType.getActualTypeArguments()[0];
|
||||
} else
|
||||
throw new ReviewedStingException("BUG: could not find generic type on class " + t);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -31,6 +31,7 @@ import org.broadinstitute.sting.commandline.ArgumentCollection;
|
|||
import org.broadinstitute.sting.commandline.CommandLineProgram;
|
||||
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
|
||||
import org.broadinstitute.sting.gatk.filters.ReadFilter;
|
||||
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;
|
||||
|
|
@ -49,7 +50,7 @@ import java.util.*;
|
|||
@DocumentedGATKFeature(
|
||||
groupName = "GATK Engine",
|
||||
summary = "Features and arguments for the GATK engine itself, available to all walkers.",
|
||||
extraDocs = { ReadFilter.class, UserException.class })
|
||||
extraDocs = { UserException.class })
|
||||
public class CommandLineGATK extends CommandLineExecutable {
|
||||
@Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
|
||||
private String analysisName = null;
|
||||
|
|
@ -174,6 +175,10 @@ public class CommandLineGATK extends CommandLineExecutable {
|
|||
StringBuilder additionalHelp = new StringBuilder();
|
||||
Formatter formatter = new Formatter(additionalHelp);
|
||||
|
||||
formatter.format("Available Reference Ordered Data types:%n");
|
||||
formatter.format(new FeatureManager().userFriendlyListOfAvailableFeatures());
|
||||
formatter.format("%n");
|
||||
|
||||
formatter.format("For a full description of this walker, see its GATKdocs at:%n");
|
||||
formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType));
|
||||
|
||||
|
|
|
|||
|
|
@ -34,7 +34,7 @@ import net.sf.samtools.SAMRecord;
|
|||
* Filter out FailsVendorQualityCheck reads.
|
||||
*/
|
||||
|
||||
public class FailsVendorQualityCheckReadFilter extends ReadFilter {
|
||||
public class FailsVendorQualityCheckFilter extends ReadFilter {
|
||||
public boolean filterOut( final SAMRecord read ) {
|
||||
return read.getReadFailsVendorQualityCheckFlag();
|
||||
}
|
||||
|
|
@ -35,7 +35,7 @@ import org.broadinstitute.sting.commandline.Argument;
|
|||
* @version 0.1
|
||||
*/
|
||||
|
||||
public class MappingQualityReadFilter extends ReadFilter {
|
||||
public class MappingQualityFilter extends ReadFilter {
|
||||
|
||||
@Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
|
||||
public int MIN_MAPPING_QUALTY_SCORE = 10;
|
||||
|
|
@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.QualityUtils;
|
|||
* @version 0.1
|
||||
*/
|
||||
|
||||
public class MappingQualityUnavailableReadFilter extends ReadFilter {
|
||||
public class MappingQualityUnavailableFilter extends ReadFilter {
|
||||
public boolean filterOut(SAMRecord rec) {
|
||||
return (rec.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE);
|
||||
}
|
||||
|
|
@ -33,7 +33,7 @@ import net.sf.samtools.SAMRecord;
|
|||
* @version 0.1
|
||||
*/
|
||||
|
||||
public class MappingQualityZeroReadFilter extends ReadFilter {
|
||||
public class MappingQualityZeroFilter extends ReadFilter {
|
||||
public boolean filterOut(SAMRecord rec) {
|
||||
return (rec.getMappingQuality() == 0);
|
||||
}
|
||||
|
|
@ -34,7 +34,7 @@ import net.sf.samtools.SAMRecord;
|
|||
* Filter out duplicate reads.
|
||||
*/
|
||||
|
||||
public class NotPrimaryAlignmentReadFilter extends ReadFilter {
|
||||
public class NotPrimaryAlignmentFilter extends ReadFilter {
|
||||
public boolean filterOut( final SAMRecord read ) {
|
||||
return read.getNotPrimaryAlignmentFlag();
|
||||
}
|
||||
|
|
@ -36,7 +36,10 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
|
|||
import org.broadinstitute.sting.utils.Utils;
|
||||
import org.broadinstitute.sting.utils.classloader.PluginManager;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
import org.broadinstitute.sting.utils.help.GATKDocUtils;
|
||||
import org.broadinstitute.sting.utils.help.HelpUtils;
|
||||
|
||||
import javax.mail.Header;
|
||||
import java.io.File;
|
||||
import java.util.*;
|
||||
|
||||
|
|
@ -50,7 +53,7 @@ import java.util.*;
|
|||
* @author depristo
|
||||
*/
|
||||
public class FeatureManager {
|
||||
public static class FeatureDescriptor {
|
||||
public static class FeatureDescriptor implements Comparable<FeatureDescriptor> {
|
||||
final String name;
|
||||
final FeatureCodec codec;
|
||||
|
||||
|
|
@ -62,6 +65,7 @@ public class FeatureManager {
|
|||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
public String getSimpleFeatureName() { return getFeatureClass().getSimpleName(); }
|
||||
public FeatureCodec getCodec() {
|
||||
return codec;
|
||||
}
|
||||
|
|
@ -70,13 +74,18 @@ public class FeatureManager {
|
|||
|
||||
@Override
|
||||
public String toString() {
|
||||
return String.format("FeatureDescriptor name=%s codec=%s feature=%s", getName(), getCodecClass().getName(), getFeatureClass().getName());
|
||||
return String.format("FeatureDescriptor name=%s codec=%s feature=%s",
|
||||
getName(), getCodecClass().getName(), getFeatureClass().getName());
|
||||
}
|
||||
|
||||
@Override
|
||||
public int compareTo(FeatureDescriptor o) {
|
||||
return getName().compareTo(o.getName());
|
||||
}
|
||||
}
|
||||
|
||||
private final PluginManager<FeatureCodec> pluginManager;
|
||||
private final Collection<FeatureDescriptor> featureDescriptors = new HashSet<FeatureDescriptor>();
|
||||
|
||||
private final Collection<FeatureDescriptor> featureDescriptors = new TreeSet<FeatureDescriptor>();
|
||||
|
||||
/**
|
||||
* Construct a FeatureManager
|
||||
|
|
@ -114,7 +123,7 @@ public class FeatureManager {
|
|||
*/
|
||||
@Requires("featureClass != null")
|
||||
public <T extends Feature> Collection<FeatureDescriptor> getByFeature(Class<T> featureClass) {
|
||||
Set<FeatureDescriptor> consistentDescriptors = new HashSet<FeatureDescriptor>();
|
||||
Set<FeatureDescriptor> consistentDescriptors = new TreeSet<FeatureDescriptor>();
|
||||
|
||||
if (featureClass == null)
|
||||
throw new IllegalArgumentException("trackRecordType value is null, please pass in an actual class object");
|
||||
|
|
@ -189,10 +198,40 @@ public class FeatureManager {
|
|||
*/
|
||||
@Ensures("result != null")
|
||||
public String userFriendlyListOfAvailableFeatures() {
|
||||
List<String> names = new ArrayList<String>();
|
||||
for ( final FeatureDescriptor descriptor : featureDescriptors )
|
||||
names.add(descriptor.getName());
|
||||
return Utils.join(",", names);
|
||||
return userFriendlyListOfAvailableFeatures(Feature.class);
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns a list of the available tribble track names (vcf,dbsnp,etc) that we can load
|
||||
* restricted to only Codecs producting Features consistent with the requiredFeatureType
|
||||
* @return
|
||||
*/
|
||||
@Ensures("result != null")
|
||||
public String userFriendlyListOfAvailableFeatures(Class<? extends Feature> requiredFeatureType) {
|
||||
final String nameHeader="Name", featureHeader = "FeatureType", docHeader="Documentation";
|
||||
|
||||
int maxNameLen = nameHeader.length(), maxFeatureNameLen = featureHeader.length();
|
||||
for ( final FeatureDescriptor descriptor : featureDescriptors ) {
|
||||
if ( requiredFeatureType.isAssignableFrom(descriptor.getFeatureClass()) ) {
|
||||
maxNameLen = Math.max(maxNameLen, descriptor.getName().length());
|
||||
maxFeatureNameLen = Math.max(maxFeatureNameLen, descriptor.getSimpleFeatureName().length());
|
||||
}
|
||||
}
|
||||
|
||||
StringBuilder docs = new StringBuilder();
|
||||
String format = "%" + maxNameLen + "s %" + maxFeatureNameLen + "s %s%n";
|
||||
docs.append(String.format(format, nameHeader, featureHeader, docHeader));
|
||||
for ( final FeatureDescriptor descriptor : featureDescriptors ) {
|
||||
if ( requiredFeatureType.isAssignableFrom(descriptor.getFeatureClass()) ) {
|
||||
String oneDoc = String.format(format,
|
||||
descriptor.getName(),
|
||||
descriptor.getSimpleFeatureName(),
|
||||
GATKDocUtils.helpLinksToGATKDocs(descriptor.getCodecClass()));
|
||||
docs.append(oneDoc);
|
||||
}
|
||||
}
|
||||
|
||||
return docs.toString();
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers;
|
|||
|
||||
import net.sf.samtools.SAMRecord;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentReadFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
|
||||
|
|
@ -17,7 +17,7 @@ import java.util.Set;
|
|||
* To change this template use File | Settings | File Templates.
|
||||
*/
|
||||
@Requires({DataSource.READS,DataSource.REFERENCE})
|
||||
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentReadFilter.class})
|
||||
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class})
|
||||
public abstract class DuplicateWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
|
||||
// Do we actually want to operate on the context?
|
||||
public boolean filter(GenomeLoc loc, AlignmentContext context, Set<List<SAMRecord>> readSets ) {
|
||||
|
|
|
|||
|
|
@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.walkers;
|
|||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.filters.DuplicateReadFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.FailsVendorQualityCheckReadFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentReadFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.FailsVendorQualityCheckFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
|
||||
|
|
@ -18,7 +18,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
|||
@By(DataSource.READS)
|
||||
@Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
|
||||
@PartitionBy(PartitionType.INTERVAL)
|
||||
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentReadFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckReadFilter.class})
|
||||
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
|
||||
public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
|
||||
// Do we actually want to operate on the context?
|
||||
public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
|
|
|
|||
|
|
@ -44,7 +44,9 @@ import java.util.Set;
|
|||
public abstract class AlleleFrequencyCalculationModel implements Cloneable {
|
||||
|
||||
public enum Model {
|
||||
/** The default model with the best performance in all cases */
|
||||
EXACT,
|
||||
/** For posterity we have kept around the older GRID_SEARCH model, but this gives inferior results and shouldn't be used. */
|
||||
GRID_SEARCH
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -53,7 +53,9 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
|
|||
}
|
||||
|
||||
public enum GENOTYPING_MODE {
|
||||
/** the default; the Unified Genotyper will choose the most likely alternate allele */
|
||||
DISCOVERY,
|
||||
/** only the alleles passed in from a VCF rod bound to the -alleles argument will be used for genotyping */
|
||||
GENOTYPE_GIVEN_ALLELES
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -36,31 +36,54 @@ import java.io.File;
|
|||
|
||||
public class UnifiedArgumentCollection {
|
||||
|
||||
// control the various models to be used
|
||||
@Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- SNP is the default option, while INDEL is also available for calling indels and BOTH is available for calling both together", required = false)
|
||||
public GenotypeLikelihoodsCalculationModel.Model GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP;
|
||||
|
||||
/**
|
||||
* Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus.
|
||||
*/
|
||||
@Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available.", required = false)
|
||||
public AlleleFrequencyCalculationModel.Model AFmodel = AlleleFrequencyCalculationModel.Model.EXACT;
|
||||
|
||||
/**
|
||||
* The expected heterozygosity value used to compute prior likelihoods for any locus. The default priors are:
|
||||
* het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2
|
||||
*/
|
||||
@Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false)
|
||||
public Double heterozygosity = DiploidSNPGenotypePriors.HUMAN_HETEROZYGOSITY;
|
||||
|
||||
@Argument(fullName = "pcr_error_rate", shortName = "pcr_error", doc = "The PCR error rate to be used for computing fragment-based likelihoods", required = false)
|
||||
public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE;
|
||||
|
||||
/**
|
||||
* Specifies how to determine the alternate allele to use for genotyping
|
||||
*/
|
||||
@Argument(fullName = "genotyping_mode", shortName = "gt_mode", doc = "Should we output confident genotypes (i.e. including ref calls) or just the variants?", required = false)
|
||||
public GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY;
|
||||
|
||||
@Argument(fullName = "output_mode", shortName = "out_mode", doc = "Should we output confident genotypes (i.e. including ref calls) or just the variants?", required = false)
|
||||
public UnifiedGenotyperEngine.OUTPUT_MODE OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY;
|
||||
|
||||
/**
|
||||
* The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with
|
||||
* confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this
|
||||
* is the default). Note that the confidence (QUAL) values for multi-sample low-pass (e.g. 4x per sample) calling might
|
||||
* be significantly smaller with the new EXACT model than with our older GRID_SEARCH model, as the latter tended to
|
||||
* over-estimate the confidence; for low-pass calling we tend to use much smaller thresholds (e.g. 4).
|
||||
*/
|
||||
@Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called", required = false)
|
||||
public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0;
|
||||
|
||||
/**
|
||||
* the minimum phred-scaled Qscore threshold to emit low confidence calls. Genotypes with confidence >= this but less
|
||||
* than the calling threshold are emitted but marked as filtered.
|
||||
*/
|
||||
@Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)", required = false)
|
||||
public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0;
|
||||
|
||||
/**
|
||||
* This argument is not enabled by default because it increases the runtime by an appreciable amount.
|
||||
*/
|
||||
@Argument(fullName = "computeSLOD", shortName = "sl", doc = "If provided, we will calculate the SLOD", required = false)
|
||||
public boolean COMPUTE_SLOD = false;
|
||||
|
||||
|
|
@ -80,7 +103,6 @@ public class UnifiedArgumentCollection {
|
|||
@Argument(fullName = "abort_at_too_much_coverage", doc = "Don't call a site if the downsampled coverage is greater than this value", required = false)
|
||||
public int COVERAGE_AT_WHICH_TO_ABORT = -1;
|
||||
|
||||
|
||||
// control the various parameters to be used
|
||||
@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
|
||||
public int MIN_BASE_QUALTY_SCORE = 17;
|
||||
|
|
@ -91,11 +113,17 @@ public class UnifiedArgumentCollection {
|
|||
@Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false)
|
||||
public Double MAX_DELETION_FRACTION = 0.05;
|
||||
|
||||
|
||||
// indel-related arguments
|
||||
/**
|
||||
* A candidate indel is genotyped (and potentially called) if there are this number of reads with a consensus indel at a site.
|
||||
* Decreasing this value will increase sensitivity but at the cost of larger calling time and a larger number of false positives.
|
||||
*/
|
||||
@Argument(fullName = "min_indel_count_for_genotyping", shortName = "minIndelCnt", doc = "Minimum number of consensus indels required to trigger genotyping run", required = false)
|
||||
public int MIN_INDEL_COUNT_FOR_GENOTYPING = 5;
|
||||
|
||||
/**
|
||||
* This argument informs the prior probability of having an indel at a site.
|
||||
*/
|
||||
@Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false)
|
||||
public double INDEL_HETEROZYGOSITY = 1.0/8000;
|
||||
|
||||
|
|
@ -126,22 +154,23 @@ public class UnifiedArgumentCollection {
|
|||
@Hidden
|
||||
@Argument(fullName = "indelDebug", shortName = "indelDebug", doc = "Output indel debug info", required = false)
|
||||
public boolean OUTPUT_DEBUG_INDEL_INFO = false;
|
||||
|
||||
@Hidden
|
||||
@Argument(fullName = "dovit", shortName = "dovit", doc = "Output indel debug info", required = false)
|
||||
public boolean dovit = false;
|
||||
|
||||
@Hidden
|
||||
@Argument(fullName = "GSA_PRODUCTION_ONLY", shortName = "GSA_PRODUCTION_ONLY", doc = "don't ever use me", required = false)
|
||||
public boolean GSA_PRODUCTION_ONLY = false;
|
||||
|
||||
@Hidden
|
||||
|
||||
@Argument(fullName = "exactCalculation", shortName = "exactCalculation", doc = "expt", required = false)
|
||||
public ExactAFCalculationModel.ExactCalculation EXACT_CALCULATION_TYPE = ExactAFCalculationModel.ExactCalculation.LINEAR_EXPERIMENTAL;
|
||||
|
||||
@Hidden
|
||||
@Argument(fullName = "ignoreSNPAlleles", shortName = "ignoreSNPAlleles", doc = "expt", required = false)
|
||||
@Argument(fullName = "ignoreSNPAlleles", shortName = "ignoreSNPAlleles", doc = "expt", required = false)
|
||||
public boolean IGNORE_SNP_ALLELES = false;
|
||||
|
||||
|
||||
@Deprecated
|
||||
@Argument(fullName="output_all_callable_bases", shortName="all_bases", doc="Please use --output_mode EMIT_ALL_SITES instead" ,required=false)
|
||||
private Boolean ALL_BASES_DEPRECATED = false;
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
|
|||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.*;
|
||||
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
|
||||
|
|
@ -45,13 +45,73 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
|||
import java.io.PrintStream;
|
||||
import java.util.*;
|
||||
|
||||
|
||||
/**
|
||||
* A variant caller which unifies the approaches of several disparate callers. Works for single-sample and
|
||||
* multi-sample data. The user can choose from several different incorporated calculation models.
|
||||
* A variant caller which unifies the approaches of several disparate callers -- Works for single-sample and multi-sample data.
|
||||
*
|
||||
* <p>
|
||||
* The GATK Unified Genotyper is a multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian genotype
|
||||
* likelihood model to estimate simultaneously the most likely genotypes and allele frequency in a population of N samples,
|
||||
* emitting an accurate posterior probability of there being a segregating variant allele at each locus as well as for the
|
||||
* genotype of each sample. The system can either emit just the variant sites or complete genotypes (which includes
|
||||
* homozygous reference calls) satisfying some phred-scaled confidence value. The genotyper can make accurate calls on
|
||||
* both single sample data and multi-sample data.
|
||||
*
|
||||
* <h2>Input</h2>
|
||||
* <p>
|
||||
* The read data from which to make variant calls.
|
||||
* </p>
|
||||
*
|
||||
* <h2>Output</h2>
|
||||
* <p>
|
||||
* A raw, unfiltered, highly specific callset in VCF format.
|
||||
* </p>
|
||||
*
|
||||
* <h2>Example generic command for multi-sample SNP calling</h2>
|
||||
* <pre>
|
||||
* java -jar GenomeAnalysisTK.jar \
|
||||
* -R resources/Homo_sapiens_assembly18.fasta \
|
||||
* -T UnifiedGenotyper \
|
||||
* -I sample1.bam [-I sample2.bam ...] \
|
||||
* --dbsnp dbSNP.vcf \
|
||||
* -o snps.raw.vcf \
|
||||
* -stand_call_conf [50.0] \
|
||||
* -stand_emit_conf 10.0 \
|
||||
* -dcov [50] \
|
||||
* [-L targets.interval_list]
|
||||
* </pre>
|
||||
*
|
||||
* <p>
|
||||
* The above command will call all of the samples in your provided BAM files [-I arguments] together and produce a VCF file
|
||||
* with sites and genotypes for all samples. The easiest way to get the dbSNP file is from the GATK resource bundle. Several
|
||||
* arguments have parameters that should be chosen based on the average coverage per sample in your data. See the detailed
|
||||
* argument descriptions below.
|
||||
* </p>
|
||||
*
|
||||
* <h2>Example command for generating calls at all sites</h2>
|
||||
* <pre>
|
||||
* java -jar /path/to/GenomeAnalysisTK.jar \
|
||||
* -l INFO \
|
||||
* -R resources/Homo_sapiens_assembly18.fasta \
|
||||
* -T UnifiedGenotyper \
|
||||
* -I /DCC/ftp/pilot_data/data/NA12878/alignment/NA12878.SLX.maq.SRP000031.2009_08.bam \
|
||||
* -o my.vcf \
|
||||
* --output_mode EMIT_ALL_SITES
|
||||
* </pre>
|
||||
*
|
||||
* <h2>Caveats</h2>
|
||||
* <ul>
|
||||
* <li>The system is under active and continuous development. All outputs, the underlying likelihood model, arguments, and
|
||||
* file formats are likely to change.</li>
|
||||
* <li>The system can be very aggressive in calling variants. In the 1000 genomes project for pilot 2 (deep coverage of ~35x)
|
||||
* we expect the raw Qscore > 50 variants to contain at least ~10% FP calls. We use extensive post-calling filters to eliminate
|
||||
* most of these FPs. Variant Quality Score Recalibration is a tool to perform this filtering.</li>
|
||||
* <li>We only handle diploid genotypes</li>
|
||||
* </ul>
|
||||
*
|
||||
*/
|
||||
|
||||
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
|
||||
@ReadFilters( {BadMateFilter.class, MappingQualityUnavailableReadFilter.class} )
|
||||
@ReadFilters( {BadMateFilter.class, MappingQualityUnavailableFilter.class} )
|
||||
@Reference(window=@Window(start=-200,stop=200))
|
||||
@By(DataSource.REFERENCE)
|
||||
@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
|
||||
|
|
@ -61,10 +121,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
|
|||
private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
|
||||
|
||||
/**
|
||||
* A dbSNP VCF file from which to annotate.
|
||||
*
|
||||
* rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
|
||||
*/
|
||||
* rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
|
||||
* dbSNP is not used in any way for the calculations themselves.
|
||||
*/
|
||||
@ArgumentCollection
|
||||
protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
|
||||
public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
|
||||
|
|
@ -72,7 +131,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
|
|||
public List<RodBinding<VariantContext>> getCompRodBindings() { return Collections.emptyList(); }
|
||||
public List<RodBinding<VariantContext>> getResourceRodBindings() { return Collections.emptyList(); }
|
||||
|
||||
// control the output
|
||||
/**
|
||||
* A raw, unfiltered, highly specific callset in VCF format.
|
||||
*/
|
||||
@Output(doc="File to which variants should be written",required=true)
|
||||
protected VCFWriter writer = null;
|
||||
|
||||
|
|
@ -82,9 +143,15 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
|
|||
@Argument(fullName = "metrics_file", shortName = "metrics", doc = "File to print any relevant callability metrics output", required = false)
|
||||
protected PrintStream metricsWriter = null;
|
||||
|
||||
/**
|
||||
* Which annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available annotations.
|
||||
*/
|
||||
@Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
|
||||
protected List<String> annotationsToUse = new ArrayList<String>();
|
||||
|
||||
/**
|
||||
* Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups.
|
||||
*/
|
||||
@Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
|
||||
protected String[] annotationClassesToUse = { "Standard" };
|
||||
|
||||
|
|
|
|||
|
|
@ -51,8 +51,11 @@ public class UnifiedGenotyperEngine {
|
|||
public static final String LOW_QUAL_FILTER_NAME = "LowQual";
|
||||
|
||||
public enum OUTPUT_MODE {
|
||||
/** the default */
|
||||
EMIT_VARIANTS_ONLY,
|
||||
/** include confident reference sites */
|
||||
EMIT_ALL_CONFIDENT_SITES,
|
||||
/** any callable site regardless of confidence */
|
||||
EMIT_ALL_SITES
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -178,6 +178,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
|
|||
* will only proceed with the realignment (even above the given threshold) if it minimizes entropy among the reads (and doesn't simply
|
||||
* push the mismatch column to another position). This parameter is just a heuristic and should be adjusted based on your particular data set.
|
||||
*/
|
||||
@Advanced
|
||||
@Argument(fullName="entropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false)
|
||||
protected double MISMATCH_THRESHOLD = 0.15;
|
||||
|
||||
|
|
@ -185,30 +186,35 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
|
|||
* For expert users only! To minimize memory consumption you can lower this number (but then the tool may skip realignment on regions with too much coverage;
|
||||
* and if the number is too low, it may generate errors during realignment). Just make sure to give Java enough memory! 4Gb should be enough with the default value.
|
||||
*/
|
||||
@Advanced
|
||||
@Argument(fullName="maxReadsInMemory", shortName="maxInMemory", doc="max reads allowed to be kept in memory at a time by the SAMFileWriter", required=false)
|
||||
protected int MAX_RECORDS_IN_MEMORY = 150000;
|
||||
|
||||
/**
|
||||
* For expert users only!
|
||||
*/
|
||||
@Advanced
|
||||
@Argument(fullName="maxIsizeForMovement", shortName="maxIsize", doc="maximum insert size of read pairs that we attempt to realign", required=false)
|
||||
protected int MAX_ISIZE_FOR_MOVEMENT = 3000;
|
||||
|
||||
/**
|
||||
* For expert users only!
|
||||
*/
|
||||
@Advanced
|
||||
@Argument(fullName="maxPositionalMoveAllowed", shortName="maxPosMove", doc="maximum positional move in basepairs that a read can be adjusted during realignment", required=false)
|
||||
protected int MAX_POS_MOVE_ALLOWED = 200;
|
||||
|
||||
/**
|
||||
* For expert users only! If you need to find the optimal solution regardless of running time, use a higher number.
|
||||
*/
|
||||
@Advanced
|
||||
@Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necessary to improve performance in deep coverage)", required=false)
|
||||
protected int MAX_CONSENSUSES = 30;
|
||||
|
||||
/**
|
||||
* For expert users only! If you need to find the optimal solution regardless of running time, use a higher number.
|
||||
*/
|
||||
@Advanced
|
||||
@Argument(fullName="maxReadsForConsensuses", shortName="greedy", doc="max reads used for finding the alternate consensuses (necessary to improve performance in deep coverage)", required=false)
|
||||
protected int MAX_READS_FOR_CONSENSUSES = 120;
|
||||
|
||||
|
|
@ -216,9 +222,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
|
|||
* For expert users only! If this value is exceeded at a given interval, realignment is not attempted and the reads are passed to the output file(s) as-is.
|
||||
* If you need to allow more reads (e.g. with very deep coverage) regardless of memory, use a higher number.
|
||||
*/
|
||||
@Advanced
|
||||
@Argument(fullName="maxReadsForRealignment", shortName="maxReads", doc="max reads allowed at an interval for realignment", required=false)
|
||||
protected int MAX_READS = 20000;
|
||||
|
||||
@Advanced
|
||||
@Argument(fullName="noOriginalAlignmentTags", shortName="noTags", required=false, doc="Don't output the original cigar or alignment start tags for each realigned read in the output bam")
|
||||
protected boolean NO_ORIGINAL_ALIGNMENT_TAGS = false;
|
||||
|
||||
|
|
@ -226,6 +234,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
|
|||
* For expert users only! This tool assumes that the target interval list is sorted; if the list turns out to be unsorted, it will throw an exception.
|
||||
* Use this argument when your interval list is not sorted to instruct the Realigner to first sort it in memory.
|
||||
*/
|
||||
@Advanced
|
||||
@Argument(fullName="targetIntervalsAreNotSorted", shortName="targetNotSorted", required=false, doc="The target intervals are not sorted")
|
||||
protected boolean TARGET_NOT_SORTED = false;
|
||||
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
|||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.filters.BadCigarFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.*;
|
||||
|
|
@ -98,7 +98,7 @@ import java.util.List;
|
|||
*
|
||||
* @author ebanks
|
||||
*/
|
||||
@ReadFilters({Platform454Filter.class, MappingQualityZeroReadFilter.class, BadCigarFilter.class})
|
||||
@ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, BadCigarFilter.class})
|
||||
@Reference(window=@Window(start=-1,stop=50))
|
||||
@Allows(value={DataSource.READS, DataSource.REFERENCE})
|
||||
@By(DataSource.REFERENCE)
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ import org.broadinstitute.sting.commandline.Tags;
|
|||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
|
||||
import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
|
||||
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
|
||||
|
|
@ -78,7 +78,7 @@ import java.util.*;
|
|||
* if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
|
||||
* only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
|
||||
*/
|
||||
@ReadFilters({Platform454Filter.class, MappingQualityZeroReadFilter.class, PlatformUnitFilter.class})
|
||||
@ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
|
||||
public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
|
||||
// @Output
|
||||
// PrintStream out;
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
|
|||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.*;
|
||||
import org.broadinstitute.sting.utils.BaseUtils;
|
||||
|
|
@ -91,7 +91,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
|
|||
@By(DataSource.READS)
|
||||
|
||||
// Filter out all reads with zero mapping quality
|
||||
@ReadFilters({MappingQualityZeroReadFilter.class})
|
||||
@ReadFilters({MappingQualityZeroFilter.class})
|
||||
|
||||
public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
|
||||
private static final boolean DEBUG = false;
|
||||
|
|
|
|||
|
|
@ -29,8 +29,8 @@ import org.broad.tribble.Feature;
|
|||
import org.broadinstitute.sting.commandline.*;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.*;
|
||||
import org.broadinstitute.sting.utils.BaseUtils;
|
||||
|
|
@ -68,6 +68,8 @@ import java.util.Map;
|
|||
*
|
||||
* <h2>Input</h2>
|
||||
* <p>
|
||||
* The input read data whose base quality scores need to be assessed.
|
||||
* <p>
|
||||
* A database of known polymorphic sites to skip over.
|
||||
* </p>
|
||||
*
|
||||
|
|
@ -95,7 +97,7 @@ import java.util.Map;
|
|||
|
||||
@BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN)
|
||||
@By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file
|
||||
@ReadFilters( {MappingQualityZeroReadFilter.class, MappingQualityUnavailableReadFilter.class} ) // Filter out all reads with zero or unavailable mapping quality
|
||||
@ReadFilters( {MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class} ) // Filter out all reads with zero or unavailable mapping quality
|
||||
@Requires( {DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES} ) // This walker requires both -I input.bam and -R reference.fasta
|
||||
@PartitionBy(PartitionType.LOCUS)
|
||||
public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.CountedData, CountCovariatesWalker.CountedData> implements TreeReducible<CountCovariatesWalker.CountedData> {
|
||||
|
|
@ -134,6 +136,10 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
|
|||
|
||||
@Argument(fullName="list", shortName="ls", doc="List the available covariates and exit", required=false)
|
||||
private boolean LIST_ONLY = false;
|
||||
|
||||
/**
|
||||
* See the -list argument to view available covariates.
|
||||
*/
|
||||
@Argument(fullName="covariate", shortName="cov", doc="Covariates to be used in the recalibration. Each covariate is given as a separate cov parameter. ReadGroup and ReportedQuality are required covariates and are already added for you.", required=false)
|
||||
private String[] COVARIATES = null;
|
||||
@Argument(fullName="standard_covs", shortName="standard", doc="Use the standard set of covariates in addition to the ones listed using the -cov argument", required=false)
|
||||
|
|
|
|||
|
|
@ -66,6 +66,8 @@ import java.util.regex.Pattern;
|
|||
*
|
||||
* <h2>Input</h2>
|
||||
* <p>
|
||||
* The input read data whose base quality scores need to be recalibrated.
|
||||
* <p>
|
||||
* The recalibration table file in CSV format that was generated by the CountCovariates walker.
|
||||
* </p>
|
||||
*
|
||||
|
|
|
|||
|
|
@ -157,6 +157,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
|
|||
*/
|
||||
@Argument(fullName="target_titv", shortName="titv", doc="The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on the optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!", required=false)
|
||||
private double TARGET_TITV = 2.15;
|
||||
|
||||
/**
|
||||
* See the input VCF file's INFO field for a list of all available annotations.
|
||||
*/
|
||||
@Argument(fullName="use_annotation", shortName="an", doc="The names of the annotations which should used for calculations", required=true)
|
||||
private String[] USE_ANNOTATIONS = null;
|
||||
|
||||
|
|
|
|||
|
|
@ -224,4 +224,14 @@ public class JVMUtils {
|
|||
throw new StingException("Unknown type: " + type + " (" + type.getClass().getName() + ")");
|
||||
}
|
||||
}
|
||||
|
||||
public static Class getParameterizedTypeClass(Type t) {
|
||||
if ( t instanceof ParameterizedType ) {
|
||||
ParameterizedType parameterizedType = (ParameterizedType)t;
|
||||
if ( parameterizedType.getActualTypeArguments().length != 1 )
|
||||
throw new ReviewedStingException("BUG: more than 1 generic type found on class" + t);
|
||||
return (Class)parameterizedType.getActualTypeArguments()[0];
|
||||
} else
|
||||
throw new ReviewedStingException("BUG: could not find generic type on class " + t);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,159 +0,0 @@
|
|||
/*
|
||||
* Copyright (c) 2010, 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.codecs.completegenomics;
|
||||
|
||||
import org.broad.tribble.Feature;
|
||||
import org.broad.tribble.FeatureCodec;
|
||||
import org.broad.tribble.readers.LineReader;
|
||||
import org.broadinstitute.sting.utils.variantcontext.Allele;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.regex.Matcher;
|
||||
import java.util.regex.Pattern;
|
||||
|
||||
/**
|
||||
* a codec for the VAR file types produced by the Complete Genomics Institute
|
||||
*/
|
||||
public class CGVarCodec implements FeatureCodec {
|
||||
|
||||
private static final String REF_TYPE = "ref";
|
||||
private static final String SNP_TYPE = "snp";
|
||||
private static final String DELETION_TYPE = "del";
|
||||
private static final String INSERTION_TYPE = "ins";
|
||||
private static final String SUBSTITUTION_TYPE = "sub";
|
||||
|
||||
// the minimum number of features in the CG file line
|
||||
private static final int minimumFeatureCount = 8;
|
||||
|
||||
/**
|
||||
* decode the location only
|
||||
* @param line the input line to decode
|
||||
* @return a HapMapFeature
|
||||
*/
|
||||
public Feature decodeLoc(String line) {
|
||||
return decode(line);
|
||||
}
|
||||
|
||||
/**
|
||||
* decode the CG record
|
||||
* @param line the input line to decode
|
||||
* @return a VariantContext
|
||||
*/
|
||||
public Feature decode(String line) {
|
||||
String[] array = line.split("\\s+");
|
||||
|
||||
// make sure the split was successful - that we got an appropriate number of fields
|
||||
if ( array.length < minimumFeatureCount )
|
||||
return null;
|
||||
|
||||
String type = array[6];
|
||||
|
||||
long start = Long.valueOf(array[4]);
|
||||
long end;
|
||||
Allele ref, alt = null;
|
||||
|
||||
//System.out.println(line);
|
||||
|
||||
if ( type.equals(SNP_TYPE) ) {
|
||||
ref = Allele.create(array[7], true);
|
||||
alt = Allele.create(array[8], false);
|
||||
end = start;
|
||||
} else if ( type.equals(INSERTION_TYPE) ) {
|
||||
ref = Allele.create(Allele.NULL_ALLELE_STRING, true);
|
||||
alt = Allele.create(array[7], false);
|
||||
end = start;
|
||||
} else if ( type.equals(DELETION_TYPE) ) {
|
||||
ref = Allele.create(array[7], true);
|
||||
alt = Allele.create(Allele.NULL_ALLELE_STRING, false);
|
||||
end = start + ref.length();
|
||||
//} else if ( type.equals(REF_TYPE) ) {
|
||||
// ref = Allele.create("N", true); // ref bases aren't accurate
|
||||
// start++;
|
||||
// end = start;
|
||||
//} else if ( type.equals(SUBSTITUTION_TYPE) ) {
|
||||
// ref = Allele.create(array[7], true);
|
||||
// alt = Allele.create(array[8], false);
|
||||
// end = start + Math.max(ref.length(), alt.length());
|
||||
} else {
|
||||
return null; // we don't handle other types
|
||||
}
|
||||
|
||||
HashSet<Allele> alleles = new HashSet<Allele>();
|
||||
alleles.add(ref);
|
||||
if ( alt != null )
|
||||
alleles.add(alt);
|
||||
|
||||
HashMap<String, Object> attrs = new HashMap<String, Object>();
|
||||
String id = array[array.length - 1];
|
||||
if ( id.indexOf("dbsnp") != -1 ) {
|
||||
attrs.put(VariantContext.ID_KEY, parseID(id));
|
||||
}
|
||||
|
||||
// create a new feature given the array
|
||||
return new VariantContext("CGI", array[3], start, end, alleles, VariantContext.NO_NEG_LOG_10PERROR, null, attrs);
|
||||
}
|
||||
|
||||
public Class<VariantContext> getFeatureType() {
|
||||
return VariantContext.class;
|
||||
}
|
||||
|
||||
// There's no spec and no character to distinguish header lines...
|
||||
private final static int NUM_HEADER_LINES = 12;
|
||||
public Object readHeader(LineReader reader) {
|
||||
return null;
|
||||
|
||||
//String headerLine = null;
|
||||
//try {
|
||||
// for (int i = 0; i < NUM_HEADER_LINES; i++)
|
||||
// headerLine = reader.readLine();
|
||||
//} catch (IOException e) {
|
||||
// throw new IllegalArgumentException("Unable to read a line from the line reader");
|
||||
//}
|
||||
//return headerLine;
|
||||
}
|
||||
|
||||
private static final Pattern DBSNP_PATTERN = Pattern.compile("^dbsnp\\.\\d+:(.*)");
|
||||
private String parseID(String raw) {
|
||||
StringBuilder sb = null;
|
||||
|
||||
String[] ids = raw.split(";");
|
||||
for ( String id : ids ) {
|
||||
Matcher matcher = DBSNP_PATTERN.matcher(id);
|
||||
if ( matcher.matches() ) {
|
||||
String rsID = matcher.group(1);
|
||||
if ( sb == null ) {
|
||||
sb = new StringBuilder(rsID);
|
||||
} else {
|
||||
sb.append(";");
|
||||
sb.append(rsID);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return sb == null ? null : sb.toString();
|
||||
}
|
||||
}
|
||||
|
|
@ -1,209 +0,0 @@
|
|||
package org.broadinstitute.sting.utils.codecs.soapsnp;
|
||||
|
||||
import org.broad.tribble.Feature;
|
||||
import org.broad.tribble.FeatureCodec;
|
||||
import org.broad.tribble.NameAwareCodec;
|
||||
import org.broad.tribble.TribbleException;
|
||||
import org.broad.tribble.exception.CodecLineParsingException;
|
||||
import org.broad.tribble.readers.LineReader;
|
||||
import org.broadinstitute.sting.utils.variantcontext.Allele;
|
||||
import org.broadinstitute.sting.utils.variantcontext.Genotype;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
/**
|
||||
* @author depristo
|
||||
* <p/>
|
||||
* a codec for parsing soapsnp files (see http://soap.genomics.org.cn/soapsnp.html#usage2)
|
||||
* <p/>
|
||||
*
|
||||
* A simple text file format with the following whitespace separated fields:
|
||||
*
|
||||
1) Chromosome ID
|
||||
2) Coordinate on chromosome, start from 1
|
||||
3) Reference genotype
|
||||
4) Consensus genotype
|
||||
5) Quality score of consensus genotype
|
||||
6) Best base
|
||||
7) Average quality score of best base
|
||||
8) Count of uniquely mapped best base
|
||||
9) Count of all mapped best base
|
||||
10) Second best bases
|
||||
11) Average quality score of second best base
|
||||
12) Count of uniquely mapped second best base
|
||||
13) Count of all mapped second best base
|
||||
14) Sequencing depth of the site
|
||||
15) Rank sum test p_value
|
||||
16) Average copy number of nearby region
|
||||
17) Whether the site is a dbSNP.
|
||||
*/
|
||||
public class SoapSNPCodec implements FeatureCodec, NameAwareCodec {
|
||||
private String[] parts;
|
||||
|
||||
// we store a name to give to each of the variant contexts we emit
|
||||
private String name = "Unknown";
|
||||
|
||||
public Feature decodeLoc(String line) {
|
||||
return decode(line);
|
||||
}
|
||||
|
||||
/**
|
||||
* Decode a line as a Feature.
|
||||
*
|
||||
* @param line
|
||||
*
|
||||
* @return Return the Feature encoded by the line, or null if the line does not represent a feature (e.g. is
|
||||
* a comment)
|
||||
*/
|
||||
public Feature decode(String line) {
|
||||
try {
|
||||
// parse into lines
|
||||
parts = line.trim().split("\\s+");
|
||||
|
||||
// check that we got the correct number of tokens in the split
|
||||
if (parts.length != 18)
|
||||
throw new CodecLineParsingException("Invalid SoapSNP row found -- incorrect element count. Expected 18, got " + parts.length + " line = " + line);
|
||||
|
||||
String contig = parts[0];
|
||||
long start = Long.valueOf(parts[1]);
|
||||
AlleleAndGenotype allelesAndGenotype = parseAlleles(parts[2], parts[3], line);
|
||||
|
||||
double negLog10PError = Integer.valueOf(parts[4]) / 10.0;
|
||||
|
||||
Map<String, Object> attributes = new HashMap<String, Object>();
|
||||
attributes.put("BestBaseQ", parts[6]);
|
||||
attributes.put("SecondBestBaseQ", parts[10]);
|
||||
attributes.put("RankSumP", parts[15]);
|
||||
// add info to keys
|
||||
|
||||
//System.out.printf("Alleles = " + allelesAndGenotype.alleles);
|
||||
//System.out.printf("genotype = " + allelesAndGenotype.genotype);
|
||||
|
||||
VariantContext vc = new VariantContext(name, contig, start, start, allelesAndGenotype.alleles, allelesAndGenotype.genotype, negLog10PError, VariantContext.PASSES_FILTERS, attributes);
|
||||
|
||||
//System.out.printf("line = %s%n", line);
|
||||
//System.out.printf("vc = %s%n", vc);
|
||||
|
||||
return vc;
|
||||
} catch (CodecLineParsingException e) {
|
||||
throw new TribbleException("Unable to parse line " + line,e);
|
||||
} catch (NumberFormatException e) {
|
||||
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
|
||||
throw new TribbleException("Unable to parse line " + line,e);
|
||||
}
|
||||
}
|
||||
|
||||
private static class AlleleAndGenotype {
|
||||
Collection<Allele> alleles;
|
||||
Collection<Genotype> genotype;
|
||||
|
||||
public AlleleAndGenotype(Collection<Allele> alleles, Genotype genotype) {
|
||||
this.alleles = alleles;
|
||||
this.genotype = new HashSet<Genotype>();
|
||||
this.genotype.add(genotype);
|
||||
}
|
||||
}
|
||||
|
||||
private AlleleAndGenotype parseAlleles(String ref, String consensusGenotype, String line) {
|
||||
/* A Adenine
|
||||
C Cytosine
|
||||
G Guanine
|
||||
T (or U) Thymine (or Uracil)
|
||||
R A or G
|
||||
Y C or T
|
||||
S G or C
|
||||
W A or T
|
||||
K G or T
|
||||
M A or C
|
||||
B C or G or T
|
||||
D A or G or T
|
||||
H A or C or T
|
||||
V A or C or G
|
||||
N any base
|
||||
. or - gap
|
||||
*/
|
||||
if ( ref.equals(consensusGenotype) )
|
||||
throw new TribbleException.InternalCodecException("Ref base and consensus genotype are the same " + ref);
|
||||
|
||||
Allele refAllele = Allele.create(ref, true);
|
||||
List<Allele> genotypeAlleles = null;
|
||||
|
||||
char base = consensusGenotype.charAt(0);
|
||||
|
||||
switch ( base ) {
|
||||
case 'A': case 'C': case 'G': case 'T':
|
||||
Allele a = Allele.create(consensusGenotype);
|
||||
genotypeAlleles = Arrays.asList(a, a);
|
||||
break;
|
||||
case 'R': case 'Y': case 'S': case 'W': case 'K': case 'M':
|
||||
genotypeAlleles = determineAlt(refAllele, ref.charAt(0), base);
|
||||
break;
|
||||
default:
|
||||
throw new TribbleException("Unexpected consensus genotype " + consensusGenotype + " at line = " + line);
|
||||
}
|
||||
|
||||
|
||||
Collection<Allele> alleles = new HashSet<Allele>(genotypeAlleles);
|
||||
alleles.add(refAllele);
|
||||
Genotype genotype = new Genotype("unknown", genotypeAlleles); // todo -- probably should include genotype quality
|
||||
|
||||
return new AlleleAndGenotype( alleles, genotype );
|
||||
}
|
||||
|
||||
private static final Map<Character, String> IUPAC_SNPS = new HashMap<Character, String>();
|
||||
static {
|
||||
IUPAC_SNPS.put('R', "AG");
|
||||
IUPAC_SNPS.put('Y', "CT");
|
||||
IUPAC_SNPS.put('S', "GC");
|
||||
IUPAC_SNPS.put('W', "AT");
|
||||
IUPAC_SNPS.put('K', "GT");
|
||||
IUPAC_SNPS.put('M', "AC");
|
||||
}
|
||||
|
||||
private List<Allele> determineAlt(Allele ref, char refbase, char alt) {
|
||||
String alts = IUPAC_SNPS.get(alt);
|
||||
if ( alts == null )
|
||||
throw new IllegalStateException("BUG: unexpected consensus genotype " + alt);
|
||||
|
||||
Allele a1 = alts.charAt(0) == refbase ? ref : Allele.create((byte)alts.charAt(0));
|
||||
Allele a2 = alts.charAt(1) == refbase ? ref : Allele.create((byte)alts.charAt(1));
|
||||
|
||||
//if ( a1 != ref && a2 != ref )
|
||||
// throw new IllegalStateException("BUG: unexpected consensus genotype " + alt + " does not contain the reference base " + ref);
|
||||
|
||||
return Arrays.asList(a1, a2);
|
||||
}
|
||||
|
||||
/**
|
||||
* @return VariantContext
|
||||
*/
|
||||
public Class<VariantContext> getFeatureType() {
|
||||
return VariantContext.class;
|
||||
}
|
||||
|
||||
public Object readHeader(LineReader reader) {
|
||||
|
||||
return null; // we don't have a meaningful header
|
||||
}
|
||||
|
||||
/**
|
||||
* get the name of this codec
|
||||
* @return our set name
|
||||
*/
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
/**
|
||||
* set the name of this codec
|
||||
* @param name new name
|
||||
*/
|
||||
public void setName(String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
||||
public static void main(String[] args) {
|
||||
System.out.printf("Testing " + args[0]);
|
||||
}
|
||||
}
|
||||
|
|
@ -39,6 +39,5 @@ public @interface DocumentedGATKFeature {
|
|||
public boolean enable() default true;
|
||||
public String groupName();
|
||||
public String summary() default "";
|
||||
public Class<? extends DocumentedGATKFeatureHandler> handler() default GenericDocumentationHandler.class;
|
||||
public Class[] extraDocs() default {};
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,55 @@
|
|||
/*
|
||||
* 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;
|
||||
|
||||
/**
|
||||
* Documentation unit. Effectively a class version of the DocumentedGATKFeature
|
||||
*
|
||||
* @author depristo
|
||||
*/
|
||||
class DocumentedGATKFeatureObject {
|
||||
private final Class classToDoc;
|
||||
private final boolean enable;
|
||||
private final String groupName, summary;
|
||||
private final Class[] extraDocs;
|
||||
|
||||
public DocumentedGATKFeatureObject(Class classToDoc, final boolean enable, final String groupName, final String summary, final Class[] extraDocs) {
|
||||
this.classToDoc = classToDoc;
|
||||
this.enable = enable;
|
||||
this.groupName = groupName;
|
||||
this.summary = summary;
|
||||
this.extraDocs = extraDocs;
|
||||
}
|
||||
|
||||
public DocumentedGATKFeatureObject(Class classToDoc, final String groupName, final String summary) {
|
||||
this(classToDoc, true, groupName, summary, new Class[]{});
|
||||
}
|
||||
|
||||
public Class getClassToDoc() { return classToDoc; }
|
||||
public boolean enable() { return enable; }
|
||||
public String groupName() { return groupName; }
|
||||
public String summary() { return summary; }
|
||||
public Class[] extraDocs() { return extraDocs; }
|
||||
}
|
||||
|
|
@ -36,9 +36,9 @@ public class GATKDocUtils {
|
|||
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");
|
||||
b.append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath);
|
||||
//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();
|
||||
}
|
||||
}
|
||||
|
|
@ -51,7 +51,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
|
|||
/** The javadoc documentation for clazz */
|
||||
final ClassDoc classDoc;
|
||||
/** The annotation that lead to this Class being in GATKDoc */
|
||||
final DocumentedGATKFeature annotation;
|
||||
final DocumentedGATKFeatureObject annotation;
|
||||
/** When was this walker built, and what's the absolute version number */
|
||||
final String buildTimestamp, absoluteVersion;
|
||||
|
||||
|
|
@ -60,7 +60,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
|
|||
Map<String, Object> forTemplate;
|
||||
|
||||
public GATKDocWorkUnit(String name, String filename, String group,
|
||||
DocumentedGATKFeature annotation, DocumentedGATKFeatureHandler handler,
|
||||
DocumentedGATKFeatureObject annotation, DocumentedGATKFeatureHandler handler,
|
||||
ClassDoc classDoc, Class clazz,
|
||||
String buildTimestamp, String absoluteVersion) {
|
||||
this.annotation = annotation;
|
||||
|
|
|
|||
|
|
@ -33,6 +33,7 @@ import freemarker.template.TemplateException;
|
|||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.log4j.Level;
|
||||
import org.apache.log4j.Logger;
|
||||
import org.broad.tribble.FeatureCodec;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
|
||||
import java.io.*;
|
||||
|
|
@ -50,6 +51,14 @@ public class GATKDoclet {
|
|||
|
||||
RootDoc rootDoc;
|
||||
|
||||
final static Collection<DocumentedGATKFeatureObject> STATIC_DOCS = new ArrayList<DocumentedGATKFeatureObject>();
|
||||
static {
|
||||
STATIC_DOCS.add(new DocumentedGATKFeatureObject(FeatureCodec.class,
|
||||
"Reference ordered data (ROD) codecs",
|
||||
"Tribble codecs for reading reference ordered data such as VCF or BED files"));
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Extracts the contents of certain types of javadoc and adds them to an XML file.
|
||||
* @param rootDoc The documentation root.
|
||||
|
|
@ -99,7 +108,7 @@ public class GATKDoclet {
|
|||
//if ( clazz != null && clazz.getName().equals("org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance"))
|
||||
// logger.debug("foo");
|
||||
|
||||
DocumentedGATKFeature feature = getFeatureForClassDoc(doc);
|
||||
DocumentedGATKFeatureObject feature = getFeatureForClassDoc(doc);
|
||||
DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
|
||||
if ( handler != null && handler.includeInDocs(doc) ) {
|
||||
logger.info("Generating documentation for class " + doc);
|
||||
|
|
@ -146,33 +155,36 @@ public class GATKDoclet {
|
|||
}
|
||||
}
|
||||
|
||||
private DocumentedGATKFeatureHandler createHandler(ClassDoc doc, DocumentedGATKFeature feature) {
|
||||
try {
|
||||
if ( feature != null ) {
|
||||
if ( feature.enable() ) {
|
||||
DocumentedGATKFeatureHandler handler = feature.handler().newInstance();
|
||||
handler.setDoclet(this);
|
||||
return handler;
|
||||
} else {
|
||||
logger.info("Skipping disabled Documentation for " + doc);
|
||||
}
|
||||
private DocumentedGATKFeatureHandler createHandler(ClassDoc doc, DocumentedGATKFeatureObject feature) {
|
||||
if ( feature != null ) {
|
||||
if ( feature.enable() ) {
|
||||
DocumentedGATKFeatureHandler handler = new GenericDocumentationHandler();
|
||||
handler.setDoclet(this);
|
||||
return handler;
|
||||
} else {
|
||||
logger.info("Skipping disabled Documentation for " + doc);
|
||||
}
|
||||
} catch ( IllegalAccessException e) {
|
||||
throw new RuntimeException(e); // the constructor is now private -- this is an error
|
||||
} catch ( InstantiationException e) {
|
||||
throw new RuntimeException(e); // the constructor is now private -- this is an error
|
||||
}
|
||||
|
||||
return null;
|
||||
}
|
||||
|
||||
private DocumentedGATKFeature getFeatureForClassDoc(ClassDoc doc) {
|
||||
// todo -- what do I need the ? extends Object to pass the compiler?
|
||||
private DocumentedGATKFeatureObject getFeatureForClassDoc(ClassDoc doc) {
|
||||
Class<? extends Object> docClass = getClassForClassDoc(doc);
|
||||
if ( docClass != null && docClass.isAnnotationPresent(DocumentedGATKFeature.class) ) {
|
||||
return docClass.getAnnotation(DocumentedGATKFeature.class);
|
||||
} else {
|
||||
|
||||
if ( docClass == null )
|
||||
return null; // not annotated so it shouldn't be documented
|
||||
|
||||
if ( docClass.isAnnotationPresent(DocumentedGATKFeature.class) ) {
|
||||
DocumentedGATKFeature f = docClass.getAnnotation(DocumentedGATKFeature.class);
|
||||
return new DocumentedGATKFeatureObject(docClass, f.enable(), f.groupName(), f.summary(), f.extraDocs());
|
||||
} else {
|
||||
for ( DocumentedGATKFeatureObject staticDocs : STATIC_DOCS ) {
|
||||
if ( staticDocs.getClassToDoc().isAssignableFrom(docClass) ) {
|
||||
return new DocumentedGATKFeatureObject(docClass, staticDocs.enable(), staticDocs.groupName(), staticDocs.summary(), staticDocs.extraDocs());
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -217,16 +229,15 @@ public class GATKDoclet {
|
|||
|
||||
Collections.sort(indexData);
|
||||
|
||||
Set<DocumentedGATKFeature> docFeatures = new HashSet<DocumentedGATKFeature>();
|
||||
List<Map<String, String>> groups = new ArrayList<Map<String, String>>();
|
||||
Set<String> seenDocumentationFeatures = new HashSet<String>();
|
||||
List<Map<String, String>> data = new ArrayList<Map<String, String>>();
|
||||
for ( GATKDocWorkUnit workUnit : indexData ) {
|
||||
data.add(workUnit.indexDataMap());
|
||||
docFeatures.add(workUnit.annotation);
|
||||
}
|
||||
|
||||
List<Map<String, String>> groups = new ArrayList<Map<String, String>>();
|
||||
for ( DocumentedGATKFeature feature : docFeatures ) {
|
||||
groups.add(toMap(feature));
|
||||
if ( ! seenDocumentationFeatures.contains(workUnit.annotation.groupName()) ) {
|
||||
groups.add(toMap(workUnit.annotation));
|
||||
seenDocumentationFeatures.add(workUnit.annotation.groupName());
|
||||
}
|
||||
}
|
||||
|
||||
root.put("data", data);
|
||||
|
|
@ -237,7 +248,7 @@ public class GATKDoclet {
|
|||
return root;
|
||||
}
|
||||
|
||||
private static final Map<String, String> toMap(DocumentedGATKFeature annotation) {
|
||||
private static final Map<String, String> toMap(DocumentedGATKFeatureObject annotation) {
|
||||
Map<String, String> root = new HashMap<String, String>();
|
||||
root.put("name", annotation.groupName());
|
||||
root.put("summary", annotation.summary());
|
||||
|
|
|
|||
|
|
@ -30,14 +30,18 @@ import com.sun.javadoc.FieldDoc;
|
|||
import com.sun.javadoc.RootDoc;
|
||||
import com.sun.javadoc.Tag;
|
||||
import org.apache.log4j.Logger;
|
||||
import org.broad.tribble.Feature;
|
||||
import org.broadinstitute.sting.commandline.*;
|
||||
import org.broadinstitute.sting.gatk.CommandLineGATK;
|
||||
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
|
||||
import org.broadinstitute.sting.utils.Utils;
|
||||
import org.broadinstitute.sting.utils.classloader.JVMUtils;
|
||||
import org.broadinstitute.sting.utils.collections.Pair;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
import org.broadinstitute.sting.utils.exceptions.StingException;
|
||||
|
||||
import java.io.*;
|
||||
import java.lang.reflect.Field;
|
||||
import java.lang.reflect.*;
|
||||
import java.util.*;
|
||||
|
||||
/**
|
||||
|
|
@ -52,13 +56,13 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
|
|||
|
||||
@Override
|
||||
public boolean includeInDocs(ClassDoc doc) {
|
||||
return true;
|
||||
// try {
|
||||
// Class type = HelpUtils.getClassForDoc(doc);
|
||||
// return JVMUtils.isConcrete(type);
|
||||
// } catch ( ClassNotFoundException e ) {
|
||||
// return false;
|
||||
// }
|
||||
// return true;
|
||||
try {
|
||||
Class type = HelpUtils.getClassForDoc(doc);
|
||||
return JVMUtils.isConcrete(type);
|
||||
} catch ( ClassNotFoundException e ) {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -107,13 +111,14 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
|
|||
// attempt to instantiate the class
|
||||
Object instance = makeInstanceIfPossible(toProcess.clazz);
|
||||
|
||||
Map<String, List<Object>> args = new HashMap<String, List<Object>>();
|
||||
Map<String, List<Map<String, Object>>> args = new HashMap<String, List<Map<String, Object>>>();
|
||||
root.put("arguments", args);
|
||||
args.put("all", new ArrayList<Object>());
|
||||
args.put("required", new ArrayList<Object>());
|
||||
args.put("optional", new ArrayList<Object>());
|
||||
args.put("hidden", new ArrayList<Object>());
|
||||
args.put("depreciated", new ArrayList<Object>());
|
||||
args.put("all", new ArrayList<Map<String, Object>>());
|
||||
args.put("required", new ArrayList<Map<String, Object>>());
|
||||
args.put("optional", new ArrayList<Map<String, Object>>());
|
||||
args.put("advanced", new ArrayList<Map<String, Object>>());
|
||||
args.put("hidden", new ArrayList<Map<String, Object>>());
|
||||
args.put("depreciated", new ArrayList<Map<String, Object>>());
|
||||
try {
|
||||
for ( ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(classdoc)) ) {
|
||||
ArgumentDefinition argDef = argumentSource.createArgumentDefinitions().get(0);
|
||||
|
|
@ -123,6 +128,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
|
|||
logger.debug(String.format("Processing %s", argumentSource));
|
||||
String kind = "optional";
|
||||
if ( argumentSource.isRequired() ) kind = "required";
|
||||
else if ( argumentSource.isAdvanced() ) kind = "advanced";
|
||||
else if ( argumentSource.isHidden() ) kind = "hidden";
|
||||
else if ( argumentSource.isDeprecated() ) kind = "depreciated";
|
||||
|
||||
|
|
@ -149,11 +155,37 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
|
|||
logger.debug(String.format("Skipping hidden feature %s", argumentSource));
|
||||
}
|
||||
}
|
||||
|
||||
// sort the arguments
|
||||
for (Map.Entry<String,List<Map<String, Object>>> entry : args.entrySet()) {
|
||||
entry.setValue(sortArguments(entry.getValue()));
|
||||
}
|
||||
} catch ( ClassNotFoundException e ) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
private List<Map<String, Object>> sortArguments(List<Map<String, Object>> unsorted) {
|
||||
Collections.sort(unsorted, new CompareArgumentsByName());
|
||||
return unsorted;
|
||||
}
|
||||
|
||||
private class CompareArgumentsByName implements Comparator<Map<String, Object>> {
|
||||
public int compare(Map<String, Object> x, Map<String, Object> y) {
|
||||
return elt(x).compareTo(elt(y));
|
||||
}
|
||||
|
||||
private String elt(Map<String, Object> m) {
|
||||
String v = m.get("name").toString().toLowerCase();
|
||||
if ( v.startsWith("--") )
|
||||
return v.substring(2);
|
||||
else if ( v.startsWith("-") )
|
||||
return v.substring(1);
|
||||
else
|
||||
throw new RuntimeException("Expect to see arguments beginning with at least one -, but found " + v);
|
||||
}
|
||||
}
|
||||
|
||||
private Object getFieldValue(Class c, Object instance, String fieldName) {
|
||||
Field field = JVMUtils.findField(c, fieldName);
|
||||
if ( field != null ) {
|
||||
|
|
@ -255,20 +287,6 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
|
|||
put("name", otherUnit.name);}});
|
||||
|
||||
}
|
||||
|
||||
List<Map<String, Object>> hierarchyDocs = new ArrayList<Map<String, Object>>();
|
||||
for (final GATKDocWorkUnit other : all ) {
|
||||
final String relation = classRelationship(toProcess.clazz, other.clazz);
|
||||
if ( relation != null )
|
||||
hierarchyDocs.add(
|
||||
new HashMap<String, Object>(){{
|
||||
put("filename", other.filename);
|
||||
put("relation", relation);
|
||||
put("name", other.name);}});
|
||||
|
||||
}
|
||||
|
||||
root.put("relatedDocs", hierarchyDocs);
|
||||
root.put("extradocs", extraDocsData);
|
||||
}
|
||||
|
||||
|
|
@ -309,6 +327,8 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
|
|||
return fieldDoc;
|
||||
|
||||
Field field = HelpUtils.getFieldForFieldDoc(fieldDoc);
|
||||
if ( field == null )
|
||||
throw new RuntimeException("Could not find the field corresponding to " + fieldDoc + ", presumably because the field is inaccessible");
|
||||
if ( field.isAnnotationPresent(ArgumentCollection.class) ) {
|
||||
ClassDoc typeDoc = getRootDoc().classNamed(fieldDoc.type().qualifiedTypeName());
|
||||
if ( typeDoc == null )
|
||||
|
|
@ -333,15 +353,82 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
|
|||
return null;
|
||||
}
|
||||
|
||||
private static final int MAX_DISPLAY_NAME = 30;
|
||||
Pair<String, String> displayNames(String s1, String s2) {
|
||||
if ( s1 == null ) return new Pair<String, String>(s2, null);
|
||||
if ( s2 == null ) return new Pair<String, String>(s1, null);
|
||||
|
||||
String l = s1.length() > s2.length() ? s1 : s2;
|
||||
String s = s1.length() > s2.length() ? s2 : s1;
|
||||
|
||||
if ( l.length() > MAX_DISPLAY_NAME )
|
||||
return new Pair<String, String>(s, l);
|
||||
else
|
||||
return new Pair<String, String>(l, s);
|
||||
}
|
||||
|
||||
protected String argumentTypeString(Type type) {
|
||||
if (type instanceof ParameterizedType) {
|
||||
ParameterizedType parameterizedType = (ParameterizedType)type;
|
||||
List<String> subs = new ArrayList<String>();
|
||||
for (Type actualType: parameterizedType.getActualTypeArguments())
|
||||
subs.add(argumentTypeString(actualType));
|
||||
return argumentTypeString(((ParameterizedType)type).getRawType()) + "[" + Utils.join(",", subs) + "]";
|
||||
} else if (type instanceof GenericArrayType) {
|
||||
return argumentTypeString(((GenericArrayType)type).getGenericComponentType()) + "[]";
|
||||
} else if (type instanceof WildcardType) {
|
||||
throw new RuntimeException("We don't support wildcards in arguments: " + type);
|
||||
} else if (type instanceof Class<?>) {
|
||||
return ((Class) type).getSimpleName();
|
||||
} else {
|
||||
throw new StingException("Unknown type: " + type);
|
||||
}
|
||||
}
|
||||
|
||||
protected Class<? extends Feature> getFeatureTypeIfPossible(Type type) {
|
||||
if ( type instanceof ParameterizedType) {
|
||||
ParameterizedType paramType = (ParameterizedType)type;
|
||||
if ( RodBinding.class.isAssignableFrom((Class<?>)paramType.getRawType()) ) {
|
||||
return (Class<? extends Feature>)JVMUtils.getParameterizedTypeClass(type);
|
||||
} else {
|
||||
for ( Type paramtype : paramType.getActualTypeArguments() ) {
|
||||
Class<? extends Feature> x = getFeatureTypeIfPossible(paramtype);
|
||||
if ( x != null )
|
||||
return x;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return null;
|
||||
}
|
||||
|
||||
protected Map<String, Object> docForArgument(FieldDoc fieldDoc, ArgumentSource source, ArgumentDefinition def) {
|
||||
Map<String, Object> root = new HashMap<String, Object>();
|
||||
root.put("name", def.shortName != null ? "-" + def.shortName : "--" + def.fullName );
|
||||
Pair<String, String> names = displayNames("-" + def.shortName, "--" + def.fullName);
|
||||
|
||||
if ( def.shortName != null && def.fullName != null )
|
||||
root.put("synonyms", "--" + def.fullName);
|
||||
root.put("name", names.getFirst() );
|
||||
|
||||
if ( names.getSecond() != null )
|
||||
root.put("synonyms", names.getSecond());
|
||||
|
||||
root.put("required", def.required ? "yes" : "no");
|
||||
root.put("type", def.argumentType.getSimpleName());
|
||||
|
||||
// type of the field
|
||||
root.put("type", argumentTypeString(source.field.getGenericType()));
|
||||
|
||||
Class<? extends Feature> featureClass = getFeatureTypeIfPossible(source.field.getGenericType());
|
||||
if ( featureClass != null ) {
|
||||
// deal with the allowable types
|
||||
FeatureManager manager = new FeatureManager();
|
||||
List<String> rodTypes = new ArrayList<String>();
|
||||
for (FeatureManager.FeatureDescriptor descriptor : manager.getByFeature(featureClass) ) {
|
||||
rodTypes.add(String.format("<a href=%s>%s</a>",
|
||||
GATKDocUtils.htmlFilenameForClass(descriptor.getCodecClass()),
|
||||
descriptor.getName()));
|
||||
}
|
||||
|
||||
root.put("rodTypes", Utils.join(", ", rodTypes));
|
||||
}
|
||||
|
||||
// summary and fulltext
|
||||
root.put("summary", def.doc != null ? def.doc : "");
|
||||
|
|
|
|||
|
|
@ -156,12 +156,13 @@ public class ListFileUtils {
|
|||
FeatureManager.FeatureDescriptor descriptor = builderForValidation.getByTriplet(triplet);
|
||||
if ( descriptor == null )
|
||||
throw new UserException.UnknownTribbleType(rodBinding.getTribbleType(),
|
||||
String.format("Field %s had provided type %s but there's no such Tribble type. Available types are %s",
|
||||
rodBinding.getName(), rodBinding.getTribbleType(), builderForValidation.userFriendlyListOfAvailableFeatures()));
|
||||
String.format("Field %s had provided type %s but there's no such Tribble type. The compatible types are: %n%s",
|
||||
rodBinding.getName(), rodBinding.getTribbleType(), builderForValidation.userFriendlyListOfAvailableFeatures(rodBinding.getType())));
|
||||
if ( ! rodBinding.getType().isAssignableFrom(descriptor.getFeatureClass()) )
|
||||
throw new UserException.BadArgumentValue(rodBinding.getName(),
|
||||
String.format("Field %s expected type %s, but the type of the input file provided on the command line was %s producing %s. Please make sure that you have provided the correct file type and/or that you are not binding your rod to a name matching one of the available types.",
|
||||
rodBinding.getName(), rodBinding.getType(), descriptor.getName(), descriptor.getFeatureClass()));
|
||||
String.format("Field %s expects Features of type %s, but the input file produces Features of type %s. The compatible types are: %n%s",
|
||||
rodBinding.getName(), rodBinding.getType().getSimpleName(), descriptor.getSimpleFeatureName(),
|
||||
builderForValidation.userFriendlyListOfAvailableFeatures(rodBinding.getType())));
|
||||
|
||||
|
||||
rodBindings.add(triplet);
|
||||
|
|
|
|||
|
|
@ -54,7 +54,8 @@ import java.util.*;
|
|||
public class FeatureManagerUnitTest extends BaseTest {
|
||||
private static final File RANDOM_FILE = new File(validationDataLocation + "exampleGATKReport.eval");
|
||||
private static final File VCF3_FILE = new File(validationDataLocation + "vcfexample3.vcf");
|
||||
private static final File VCF4_FILE = new File(validationDataLocation + "vcf4.1.example.vcf");
|
||||
private static final File VCF4_FILE = new File(testDir + "HiSeq.10000.vcf");
|
||||
private static final File VCF4_FILE_GZ = new File(testDir + "HiSeq.10000.vcf.gz");
|
||||
|
||||
private FeatureManager manager;
|
||||
private GenomeLocParser genomeLocParser;
|
||||
|
|
@ -98,7 +99,8 @@ public class FeatureManagerUnitTest extends BaseTest {
|
|||
}
|
||||
|
||||
public String toString() {
|
||||
return String.format("FMTest name=%s codec=%s feature=%s file=%s", name, codec, feature, associatedFile);
|
||||
return String.format("FMTest name=%s codec=%s feature=%s file=%s",
|
||||
name, codec.getSimpleName(), feature.getSimpleName(), associatedFile);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -106,6 +108,7 @@ public class FeatureManagerUnitTest extends BaseTest {
|
|||
public Object[][] createTests() {
|
||||
new FMTest(VariantContext.class, VCF3Codec.class, "VCF3", VCF3_FILE);
|
||||
new FMTest(VariantContext.class, VCFCodec.class, "VCF", VCF4_FILE);
|
||||
new FMTest(VariantContext.class, VCFCodec.class, "VCF", VCF4_FILE_GZ);
|
||||
new FMTest(TableFeature.class, BedTableCodec.class, "bedtable", null);
|
||||
return FMTest.getTests(FMTest.class);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -38,21 +38,21 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
|
|||
return "-T CombineVariants -NO_HEADER -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
|
||||
}
|
||||
|
||||
public void test1InOut(String file, String md5, boolean vcf3) {
|
||||
test1InOut(file, md5, "", vcf3);
|
||||
public void test1InOut(String file, String md5) {
|
||||
test1InOut(file, md5, "");
|
||||
}
|
||||
|
||||
public void test1InOut(String file, String md5, String args, boolean vcf3) {
|
||||
public void test1InOut(String file, String md5, String args) {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(" -priority v1 -V:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file + args),
|
||||
baseTestString(" -priority v1 -V:v1 " + validationDataLocation + file + args),
|
||||
1,
|
||||
Arrays.asList(md5));
|
||||
executeTest("testInOut1--" + file, spec);
|
||||
}
|
||||
|
||||
public void combine2(String file1, String file2, String args, String md5, boolean vcf3) {
|
||||
public void combine2(String file1, String file2, String args, String md5) {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(" -priority v1,v2 -V:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file1 + " -V:v2,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file2 + args),
|
||||
baseTestString(" -priority v1,v2 -V:v1 " + validationDataLocation + file1 + " -V:v2 "+ validationDataLocation + file2 + args),
|
||||
1,
|
||||
Arrays.asList(md5));
|
||||
executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
|
||||
|
|
@ -78,23 +78,23 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
|
|||
executeTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
|
||||
}
|
||||
|
||||
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "c608b9fc1e36dba6cebb4f259883f9f0", true); }
|
||||
@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "20caad94411d6ab48153b214de916df8", " -setKey foo", true); }
|
||||
@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "004f3065cb1bc2ce2f9afd695caf0b48", " -setKey null", true); }
|
||||
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "c9c901ff9ef2a982624b203a8086dff0", false); } // official project VCF files in tabix format
|
||||
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "c608b9fc1e36dba6cebb4f259883f9f0"); }
|
||||
@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "20caad94411d6ab48153b214de916df8", " -setKey foo"); }
|
||||
@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "004f3065cb1bc2ce2f9afd695caf0b48", " -setKey null"); }
|
||||
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "c9c901ff9ef2a982624b203a8086dff0"); } // official project VCF files in tabix format
|
||||
|
||||
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "7593be578d4274d672fc22fced38012b", false); }
|
||||
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "1cd467863c4e948fadd970681552d57e", false); }
|
||||
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "7593be578d4274d672fc22fced38012b"); }
|
||||
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "1cd467863c4e948fadd970681552d57e"); }
|
||||
|
||||
@Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "0f873fed02aa99db5b140bcd6282c10a"); }
|
||||
|
||||
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "1d5a021387a8a86554db45a29f66140f", false); } // official project VCF files in tabix format
|
||||
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "20163d60f18a46496f6da744ab5cc0f9", false); } // official project VCF files in tabix format
|
||||
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f1cf095c2fe9641b7ca1f8ee2c46fd4a", false); }
|
||||
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "1d5a021387a8a86554db45a29f66140f"); } // official project VCF files in tabix format
|
||||
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "20163d60f18a46496f6da744ab5cc0f9"); } // official project VCF files in tabix format
|
||||
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f1cf095c2fe9641b7ca1f8ee2c46fd4a"); }
|
||||
|
||||
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e144b6283765494bfe8189ac59965083", false); }
|
||||
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e144b6283765494bfe8189ac59965083"); }
|
||||
|
||||
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c", true); }
|
||||
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c"); }
|
||||
|
||||
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "4836086891f6cbdd40eebef3076d215a"); }
|
||||
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "6a34b5d743efda8b2f3b639f3a2f5de8"); }
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -20,16 +20,21 @@
|
|||
<#macro argumentDetails arg>
|
||||
<h3><a name="${arg.name}">${arg.name}<#if arg.synonyms??> / ${arg.synonyms}</#if></a>
|
||||
(<#if arg.attributes??>${arg.attributes} </#if>${arg.type}<#if arg.defaultValue??> with default value ${arg.defaultValue}</#if>)</h3>
|
||||
${arg.summary}. ${arg.fulltext}<br>
|
||||
<p class="args">
|
||||
${arg.summary}. ${arg.fulltext}
|
||||
<#if arg.rodTypes??>${arg.name} binds reference ordered data. This argument supports ROD files of the
|
||||
following types: ${arg.rodTypes}</#if>
|
||||
<#if arg.options??>
|
||||
<p>The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:</p>
|
||||
<br>
|
||||
The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:
|
||||
<dl class="enum">
|
||||
<#list arg.options as option>
|
||||
<dt>${option.name}
|
||||
<dd>${option.summary}
|
||||
<dt class="enum">${option.name}</dt>
|
||||
<dd class="enum">${option.summary}</dd>
|
||||
</#list>
|
||||
</dl>
|
||||
</#if>
|
||||
</p>
|
||||
</#macro>
|
||||
|
||||
<#macro relatedByType name type>
|
||||
|
|
@ -77,6 +82,7 @@
|
|||
<tbody>
|
||||
<@argumentlist name="Required" myargs=arguments.required/>
|
||||
<@argumentlist name="Optional" myargs=arguments.optional/>
|
||||
<@argumentlist name="Advanced" myargs=arguments.advanced/>
|
||||
<@argumentlist name="Hidden" myargs=arguments.hidden/>
|
||||
<@argumentlist name="Depreciated" myargs=arguments.depreciated/>
|
||||
</tbody>
|
||||
|
|
@ -98,7 +104,7 @@
|
|||
</#if>
|
||||
|
||||
<#-- This class is related to other documented classes via sub/super relationships -->
|
||||
<#if relatedDocs?size != 0>
|
||||
<#if relatedDocs?? && relatedDocs?size != 0>
|
||||
<hr>
|
||||
<h2>Related capabilities</h2>
|
||||
<@relatedByType name="Superclasses" type="superclass"/>
|
||||
|
|
|
|||
|
|
@ -42,6 +42,10 @@ p.version
|
|||
text-align: center;
|
||||
}
|
||||
|
||||
p.args
|
||||
{
|
||||
margin-left: 3em;
|
||||
}
|
||||
|
||||
h1, h2, h3, h4
|
||||
{
|
||||
|
|
@ -81,17 +85,17 @@ hr
|
|||
* enum DT layout
|
||||
*/
|
||||
|
||||
dl {
|
||||
border: 1px solid #ccc;
|
||||
dl.enum {
|
||||
margin-left: 3em;
|
||||
border: 1px dashed #ccc;
|
||||
}
|
||||
|
||||
dt {
|
||||
dt.enum {
|
||||
font-weight: bold;
|
||||
text-decoration: underline;
|
||||
}
|
||||
|
||||
dd {
|
||||
margin: 0;
|
||||
dd.enum {
|
||||
padding: 0 0 0.5em 0;
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue