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Moved getMetaDataForField to VariantContextUtils

This commit is contained in:
Mark DePristo 2012-05-22 07:14:46 -04:00
parent cb13f16e90
commit 69ee4d0454
5 changed files with 34 additions and 22 deletions
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7
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
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@ -37,10 +37,7 @@ import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.sting.utils.variantcontext.*;
import java.io.ByteArrayInputStream;
import java.io.FileInputStream;
@ -292,7 +289,7 @@ public class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceDepende
for ( int i = 0; i < numInfoFields; i++ ) {
final String key = getDictionaryString();
Object value = decoder.decodeTypedValue();
final VCFCompoundHeaderLine metaData = VariantContext.getMetaDataForField(header, key);
final VCFCompoundHeaderLine metaData = VariantContextUtils.getMetaDataForField(header, key);
if ( metaData.getType() == VCFHeaderLineType.Flag ) value = true; // special case for flags
infoFieldEntries.put(key, value);
}

15
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -3,11 +3,8 @@ package org.broadinstitute.sting.utils.variantcontext;
import org.broad.tribble.Feature;
import org.broad.tribble.TribbleException;
import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.*;
@ -1295,7 +1292,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
for ( final Map.Entry<String, Object> attr : attributes.entrySet() ) {
final String field = attr.getKey();
final VCFCompoundHeaderLine format = getMetaDataForField(header, field);
final VCFCompoundHeaderLine format = VariantContextUtils.getMetaDataForField(header, field);
final Object decoded = decodeValue(field, attr.getValue(), format);
if ( decoded != null )
@ -1359,14 +1356,6 @@ public class VariantContext implements Feature { // to enable tribble integratio
return new Genotype(g.getSampleName(), g.getAlleles(), g.getLog10PError(), g.getFilters(), map, g.isPhased());
}
public final static VCFCompoundHeaderLine getMetaDataForField(final VCFHeader header, final String field) {
VCFCompoundHeaderLine metaData = header.getFormatHeaderLine(field);
if ( metaData == null ) metaData = header.getInfoHeaderLine(field);
if ( metaData == null )
throw new UserException.MalformedVCF("Fully decoding VariantContext requires header line for all fields, but none was found for " + field);
return metaData;
}
// ---------------------------------------------------------------------------------------------------------
//
// tribble integration routines -- not for public consumption

19
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
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@ -49,6 +49,7 @@ public class VariantContextUtils {
final public static JexlEngine engine = new JexlEngine();
public static final int DEFAULT_PLOIDY = 2;
private final static boolean ASSUME_MISSING_FIELDS_ARE_STRINGS = true;
static {
engine.setSilent(false); // will throw errors now for selects that don't evaluate properly
@ -268,6 +269,24 @@ public class VariantContextUtils {
}
private static Set<String> MISSING_KEYS_WARNED_ABOUT = new HashSet<String>();
public final static VCFCompoundHeaderLine getMetaDataForField(final VCFHeader header, final String field) {
VCFCompoundHeaderLine metaData = header.getFormatHeaderLine(field);
if ( metaData == null ) metaData = header.getInfoHeaderLine(field);
if ( metaData == null ) {
if ( ASSUME_MISSING_FIELDS_ARE_STRINGS ) {
if ( ! MISSING_KEYS_WARNED_ABOUT.contains(field) ) {
MISSING_KEYS_WARNED_ABOUT.add(field);
logger.warn("Field " + field + " missing from VCF header, assuming it is an unbounded string type");
}
return new VCFInfoHeaderLine(field, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Auto-generated string header for " + field);
}
else
throw new UserException.MalformedVCF("Fully decoding VariantContext requires header line for all fields, but none was found for " + field);
}
return metaData;
}
/**
* A simple but common wrapper for matching VariantContext objects using JEXL expressions
*/

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
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@ -226,7 +226,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
}
private final int getNGenotypeFieldValues(final String field, final VariantContext vc) {
final VCFCompoundHeaderLine metaData = VariantContext.getMetaDataForField(header, field);
final VCFCompoundHeaderLine metaData = VariantContextUtils.getMetaDataForField(header, field);
assert metaData != null; // field is supposed to be in header
int nFields = metaData.getCount(vc.getNAlleles() - 1);
@ -298,7 +298,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
// TODO -- need to generalize so we can enable vectors of compressed genotype ints
// TODO -- no sense in allocating these over and over
private final VCFToBCFEncoding prepFieldValueForEncoding(final String field, final Object value) {
final VCFCompoundHeaderLine metaData = VariantContext.getMetaDataForField(header, field);
final VCFCompoundHeaderLine metaData = VariantContextUtils.getMetaDataForField(header, field);
final boolean isList = value instanceof List;
final Object toType = isList ? ((List)value).get(0) : value;

11
public/java/test/org/broadinstitute/sting/WalkerTest.java
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@ -47,7 +47,7 @@ import java.io.IOException;
import java.util.*;
public class WalkerTest extends BaseTest {
private static final boolean GENERATE_SHADOW_BCF = false;
private static final boolean GENERATE_SHADOW_BCF = true;
private static final boolean ENABLE_PHONE_HOME_FOR_TESTS = false;
private static final boolean ENABLE_ON_THE_FLY_CHECK_FOR_VCF_INDEX = false;
@ -144,6 +144,7 @@ public class WalkerTest extends BaseTest {
List<String> exts = null;
Class expectedException = null;
boolean includeImplicitArgs = true;
boolean includeShadowBCF = true;
// the default output path for the integration test
private File outputFileLocation = null;
@ -183,13 +184,19 @@ public class WalkerTest extends BaseTest {
args = args + (ENABLE_PHONE_HOME_FOR_TESTS ?
String.format(" -et %s ", GATKRunReport.PhoneHomeOption.STANDARD) :
String.format(" -et %s -K %s ", GATKRunReport.PhoneHomeOption.NO_ET, gatkKeyFile));
if ( GENERATE_SHADOW_BCF )
if ( includeShadowBCF && GENERATE_SHADOW_BCF )
args = args + " --generateShadowBCF ";
}
return args;
}
/**
* In the case where the input VCF files are malformed and cannot be fixed
* this function tells the engine to not try to generate a shadow BCF
* which will ultimately blow up...
*/
public void disableShadowBCF() { this.includeShadowBCF = false; }
public void setOutputFileLocation(File outputFileLocation) {
this.outputFileLocation = outputFileLocation;
}