/*
* Copyright (c) 2012 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 htsjdk.variant.variantcontext.writer;
import htsjdk.variant.utils.GeneralUtils;
import htsjdk.variant.vcf.VCFCompoundHeaderLine;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFFormatHeaderLine;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import java.util.HashMap;
import java.util.Map;
/**
* See #BCFWriter for documentation on this classes role in encoding BCF2 files
*
* @author Mark DePristo
* @since 06/12
*/
public class BCF2FieldWriterManager {
final Map<String, BCF2FieldWriter.SiteWriter> siteWriters = new HashMap<String, BCF2FieldWriter.SiteWriter>();
final Map<String, BCF2FieldWriter.GenotypesWriter> genotypesWriters = new HashMap<String, BCF2FieldWriter.GenotypesWriter>();
final IntGenotypeFieldAccessors intGenotypeFieldAccessors = new IntGenotypeFieldAccessors();
public BCF2FieldWriterManager() { }
/**
* Setup the FieldWriters appropriate to each INFO and FORMAT in the VCF header
*
* Must be called before any of the getter methods will work
*
* @param header a VCFHeader containing description for every INFO and FORMAT field we'll attempt to write out to BCF
* @param encoder the encoder we are going to use to write out the BCF2 data
* @param stringDictionary a map from VCFHeader strings to their offsets for encoding
*/
public void setup(final VCFHeader header, final BCF2Encoder encoder, final Map<String, Integer> stringDictionary) {
for (final VCFInfoHeaderLine line : header.getInfoHeaderLines()) {
final String field = line.getID();
final BCF2FieldWriter.SiteWriter writer = createInfoWriter(header, line, encoder, stringDictionary);
add(siteWriters, field, writer);
}
for (final VCFFormatHeaderLine line : header.getFormatHeaderLines()) {
final String field = line.getID();
final BCF2FieldWriter.GenotypesWriter writer = createGenotypesWriter(header, line, encoder, stringDictionary);
add(genotypesWriters, field, writer);
}
}
private final <T> void add(final Map<String, T> map, final String field, final T writer) {
if ( map.containsKey(field) )
throw new IllegalStateException("BUG: field " + field + " already seen in VCFHeader while building BCF2 field encoders");
map.put(field, writer);
}
// -----------------------------------------------------------------
//
// Master routine to look at the header, a specific line, and
// build an appropriate SiteWriter for that header element
//
// -----------------------------------------------------------------
private BCF2FieldWriter.SiteWriter createInfoWriter(final VCFHeader header,
final VCFInfoHeaderLine line,
final BCF2Encoder encoder,
final Map<String, Integer> dict) {
return new BCF2FieldWriter.GenericSiteWriter(header, createFieldEncoder(line, encoder, dict, false));
}
private BCF2FieldEncoder createFieldEncoder(final VCFCompoundHeaderLine line,
final BCF2Encoder encoder,
final Map<String, Integer> dict,
final boolean createGenotypesEncoders ) {
if ( createGenotypesEncoders && intGenotypeFieldAccessors.getAccessor(line.getID()) != null ) {
if ( GeneralUtils.DEBUG_MODE_ENABLED && line.getType() != VCFHeaderLineType.Integer )
System.err.println("Warning: field " + line.getID() + " expected to encode an integer but saw " + line.getType() + " for record " + line);
return new BCF2FieldEncoder.IntArray(line, dict);
} else if ( createGenotypesEncoders && line.getID().equals(VCFConstants.GENOTYPE_KEY) ) {
return new BCF2FieldEncoder.GenericInts(line, dict);
} else {
switch ( line.getType() ) {
case Character:
case String:
return new BCF2FieldEncoder.StringOrCharacter(line, dict);
case Flag:
return new BCF2FieldEncoder.Flag(line, dict);
case Float:
return new BCF2FieldEncoder.Float(line, dict);
case Integer:
if ( line.isFixedCount() && line.getCount() == 1 )
return new BCF2FieldEncoder.AtomicInt(line, dict);
else
return new BCF2FieldEncoder.GenericInts(line, dict);
default:
throw new IllegalArgumentException("Unexpected type for field " + line.getID());
}
}
}
// -----------------------------------------------------------------
//
// Master routine to look at the header, a specific line, and
// build an appropriate Genotypes for that header element
//
// -----------------------------------------------------------------
private BCF2FieldWriter.GenotypesWriter createGenotypesWriter(final VCFHeader header,
final VCFFormatHeaderLine line,
final BCF2Encoder encoder,
final Map<String, Integer> dict) {
final String field = line.getID();
final BCF2FieldEncoder fieldEncoder = createFieldEncoder(line, encoder, dict, true);
if ( field.equals(VCFConstants.GENOTYPE_KEY) ) {
return new BCF2FieldWriter.GTWriter(header, fieldEncoder);
} else if ( line.getID().equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
return new BCF2FieldWriter.FTGenotypesWriter(header, fieldEncoder);
} else if ( intGenotypeFieldAccessors.getAccessor(field) != null ) {
return new BCF2FieldWriter.IGFGenotypesWriter(header, fieldEncoder, intGenotypeFieldAccessors.getAccessor(field));
} else if ( line.getType() == VCFHeaderLineType.Integer ) {
return new BCF2FieldWriter.IntegerTypeGenotypesWriter(header, fieldEncoder);
} else {
return new BCF2FieldWriter.StaticallyTypeGenotypesWriter(header, fieldEncoder);
}
}
// -----------------------------------------------------------------
//
// Accessors to get site / genotype writers
//
// -----------------------------------------------------------------
/**
* Get a site writer specialized to encode values for site info field
* @param field key found in the VCF header INFO records
* @return non-null writer if one can be found, or null if none exists for field
*/
public BCF2FieldWriter.SiteWriter getSiteFieldWriter(final String field) {
return getWriter(field, siteWriters);
}
/**
* Get a genotypes writer specialized to encode values for genotypes field
* @param field key found in the VCF header FORMAT records
* @return non-null writer if one can be found, or null if none exists for field
*/
public BCF2FieldWriter.GenotypesWriter getGenotypeFieldWriter(final String field) {
return getWriter(field, genotypesWriters);
}
public <T> T getWriter(final String key, final Map<String, T> map) {
return map.get(key);
}
}