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Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly.

This commit is contained in:
Eric Banks 2011-11-09 15:24:29 -05:00
parent 66ad2b941c
commit d64f8a89a9
11 changed files with 20 additions and 65 deletions
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48
public/java/src/org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.java
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@ -1,48 +0,0 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata;
import java.io.File;
/**
* An interface marking that a given Tribble codec can look at the file and determine whether the
* codec specifically parsing the contents of the file.
*/
public interface SelfScopingFeatureCodec {
/**
* This function returns true iff the File potentialInput can be parsed by this
* codec.
*
* The GATK assumes that there's never a situation where two SelfScopingFeaetureCodecs
* return true for the same file. If this occurs the GATK splits out an error.
*
* Note this function must never throw an error. All errors should be trapped
* and false returned.
*
* @param potentialInput the file to test for parsiability with this codec
* @return true if potentialInput can be parsed, false otherwise
*/
public boolean canDecode(final File potentialInput);
}

10
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
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@ -30,16 +30,12 @@ import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.NameAwareCodec;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
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.*;
@ -159,10 +155,8 @@ public class FeatureManager {
public FeatureDescriptor getByFiletype(File file) {
List<FeatureDescriptor> canParse = new ArrayList<FeatureDescriptor>();
for ( FeatureDescriptor descriptor : featureDescriptors )
if ( descriptor.getCodec() instanceof SelfScopingFeatureCodec ) {
if ( ((SelfScopingFeatureCodec) descriptor.getCodec()).canDecode(file) ) {
canParse.add(descriptor);
}
if ( descriptor.getCodec().canDecode(file) ) {
canParse.add(descriptor);
}
if ( canParse.size() == 0 )

2
public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
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@ -249,4 +249,6 @@ public class BeagleCodec implements ReferenceDependentFeatureCodec<BeagleFeature
return bglFeature;
}
public boolean canDecode(final File potentialInput) { return false; }
}

4
public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
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@ -24,8 +24,8 @@
package org.broadinstitute.sting.utils.codecs.hapmap;
import org.broad.tribble.AbstractFeatureCodec;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.annotation.Strand;
import org.broad.tribble.readers.LineReader;
@ -71,7 +71,7 @@ import java.util.Arrays;
* @author Mark DePristo
* @since 2010
*/
public class RawHapMapCodec implements FeatureCodec {
public class RawHapMapCodec extends AbstractFeatureCodec {
// the minimum number of features in the HapMap file line
private static final int minimumFeatureCount = 11;

4
public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
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@ -9,6 +9,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;
import java.util.ArrayList;
/**
@ -138,4 +139,7 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
public Class<RefSeqFeature> getFeatureType() {
return RefSeqFeature.class;
}
public boolean canDecode(final File potentialInput) { return false; }
}

4
public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
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@ -25,8 +25,8 @@
package org.broadinstitute.sting.utils.codecs.sampileup;
import org.broad.tribble.AbstractFeatureCodec;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.exception.CodecLineParsingException;
import org.broad.tribble.readers.LineReader;
import org.broad.tribble.util.ParsingUtils;
@ -76,7 +76,7 @@ import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.V
* @author Matt Hanna
* @since 2009
*/
public class SAMPileupCodec implements FeatureCodec<SAMPileupFeature> {
public class SAMPileupCodec extends AbstractFeatureCodec<SAMPileupFeature> {
// the number of tokens we expect to parse from a pileup line
private static final int expectedTokenCount = 10;
private static final char fldDelim = '\t';

4
public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
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@ -27,8 +27,8 @@ package org.broadinstitute.sting.utils.codecs.samread;
import net.sf.samtools.Cigar;
import net.sf.samtools.TextCigarCodec;
import net.sf.samtools.util.StringUtil;
import org.broad.tribble.AbstractFeatureCodec;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.exception.CodecLineParsingException;
import org.broad.tribble.readers.LineReader;
import org.broad.tribble.util.ParsingUtils;
@ -52,7 +52,7 @@ import org.broad.tribble.util.ParsingUtils;
* @author Matt Hanna
* @since 2009
*/
public class SAMReadCodec implements FeatureCodec<SAMReadFeature> {
public class SAMReadCodec extends AbstractFeatureCodec<SAMReadFeature> {
/* SL-XBC:1:10:628:923#0 16 Escherichia_coli_K12 1 37 76M = 1 0 AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGA B@>87<;A@?@957:>>@AA@B>@A9AB@B>@A@@@@@A;=AAB@BBBBBCBBBB@>A>:ABB@BAABCB=CA@CB */
// the number of tokens we expect to parse from a read line

4
public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
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@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
@ -101,4 +102,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
}
return header;
}
public boolean canDecode(final File potentialInput) { return false; }
}

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -8,7 +8,6 @@ import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.LineReader;
import org.broad.tribble.util.BlockCompressedInputStream;
import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -20,7 +19,7 @@ import java.util.*;
import java.util.zip.GZIPInputStream;
public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, VCFParser, SelfScopingFeatureCodec {
public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, VCFParser {
protected final static Logger log = Logger.getLogger(VCFCodec.class);
protected final static int NUM_STANDARD_FIELDS = 8; // INFO is the 8th column

BIN
settings/repository/org.broad/tribble-40.jar → settings/repository/org.broad/tribble-41.jar
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2
settings/repository/org.broad/tribble-40.xml → settings/repository/org.broad/tribble-41.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="40" status="integration" />
<info organisation="org.broad" module="tribble" revision="41" status="integration" />
</ivy-module>