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removing non-ascii characters from my Copyright and from VariantEval2Walker 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2856 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-02-18 18:54:36 +00:00
parent 33ae256186
commit b1a4e6d840
15 changed files with 58 additions and 26 deletions
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30
java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
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@ -1,6 +1,9 @@
package org.broadinstitute.sting.gatk.refdata;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
import org.broadinstitute.sting.gatk.refdata.tracks.RODRMDTrack;
import org.broadinstitute.sting.oneoffprojects.refdata.HapmapVCFROD;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
@ -17,7 +20,7 @@ import java.util.*;
* Time: 10:47:14 AM
* To change this template use File | Settings | File Templates.
*/
public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements Iterable<RODRecordList<ROD>> {
public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements Iterable<RODRecordList<ROD>> { // }, RMDTrackBuilder {
private String name;
private File file = null;
// private String fieldDelimiter;
@ -30,6 +33,31 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
/** our log, which we want to capture anything from this class */
private static Logger logger = Logger.getLogger(ReferenceOrderedData.class);
/** @return a map of all available tracks we currently have access to create */
//@Override
public Map<String, Class> getAvailableTrackNamesAndTypes() {
Map<String, Class> ret = new HashMap<String, Class>();
for (RODBinding binding: Types.values())
ret.put(binding.name, binding.type);
return ret;
}
/**
* create a RMDTrack of the specified type
*
* @param targetClass the target class of track
* @param name what to call the track
* @param inputFile the input file
*
* @return an instance of the track
* @throws org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException
* if we don't know of the target class or we couldn't create it
*/
//@Override
public RMDTrack createInstanceOfTrack(Class targetClass, String name, File inputFile) throws RMDTrackCreationException {
return new RODRMDTrack(targetClass, name, inputFile, parse1Binding(name,targetClass.getName(),inputFile.getAbsolutePath()));
}
// ----------------------------------------------------------------------
//

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureReaderTrack.java
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@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java
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@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
View File

@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java
View File

@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManager.java
View File

@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/RODRMDTrack.java
View File

@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
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@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
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@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
View File

@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
View File

@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/src/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java
View File

@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

28
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
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@ -1,23 +1,27 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.MutableVariantContext;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.PackageUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.xReadLines;
import java.util.*;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.io.File;
import java.io.FileNotFoundException;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.util.*;
// todo -- evalations should support comment lines
// todo -- add Mendelian variable explanations (nDeNovo and nMissingTransmissions)
@ -71,9 +75,9 @@ import java.io.FileNotFoundException;
// todo Assume that the incoming VCF has the annotations (you don't need to do this) but VE2 should split up results by
// todo these catogies automatically (using the default selects)
//
// todo -- We agreed to report two standard values for variant evaluation from Êhere out. ÊOne, we will continue to report
// todo -- We agreed to report two standard values for variant evaluation from here out. One, we will continue to report
// todo -- the dbSNP 129 rate. Additionally, we will start to report the % of variants found that have already been seen in
// todo -- 1000 Genomes. ÊThis should be implemented as another standard comp_1kg binding, pointing to only variants
// todo -- 1000 Genomes. This should be implemented as another standard comp_1kg binding, pointing to only variants
// todo -- discovered and released by 1KG. Might need to make this data set ourselves and keep it in GATK/data like
// todo -- dbsnp rod
//

2
java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerTest.java
View File

@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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

2
java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderTest.java
View File

@ -2,7 +2,7 @@
* 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
* Þles (the ÓSoftwareÓ), to deal in the Software without
* 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