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/*
* 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.vcf;
import htsjdk.tribble.TribbleException;
import htsjdk.variant.utils.GeneralUtils;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.Map;
import java.util.Set;
/**
* Manages header lines for standard VCF
INFO
and
FORMAT
fields.
*
* Provides simple mechanisms for
* 1) registering standard lines,
* 2) looking them up, and
* 3) adding them to headers.
*
* @author Mark DePristo
* @since 6/12
*/
public class VCFStandardHeaderLines {
/**
* Enabling this causes us to repair header lines even if only their descriptions differ.
*/
private final static boolean REPAIR_BAD_DESCRIPTIONS = false;
private static Standards formatStandards = new Standards();
private static Standards infoStandards = new Standards();
/**
* Walks over the VCF header and repairs the standard VCF header lines in it, returning a freshly
* allocated {@link VCFHeader} with standard VCF header lines repaired as necessary.
*/
public static VCFHeader repairStandardHeaderLines(final VCFHeader oldHeader) {
final Set newLines = new LinkedHashSet(oldHeader.getMetaDataInInputOrder().size());
for ( VCFHeaderLine line : oldHeader.getMetaDataInInputOrder() ) {
if ( line instanceof VCFFormatHeaderLine ) {
line = formatStandards.repair((VCFFormatHeaderLine) line);
} else if ( line instanceof VCFInfoHeaderLine) {
line = infoStandards.repair((VCFInfoHeaderLine) line);
}
newLines.add(line);
}
final VCFHeader repairedHeader = new VCFHeader(newLines, oldHeader.getGenotypeSamples());
final VCFHeaderVersion oldHeaderVersion = oldHeader.getVCFHeaderVersion();
if (oldHeaderVersion != null && oldHeaderVersion.isAtLeastAsRecentAs(VCFHeaderVersion.VCF4_3)) {
// this needs to maintain version 4.3 (and not back-version to v4.2), so propagate
// the old version only for v4.3
repairedHeader.setVCFHeaderVersion(oldHeaderVersion);
}
return repairedHeader;
}
/**
* Adds header lines for each of the format fields in IDs to header, returning the set of
* {@code IDs} without standard descriptions, unless {@code throwErrorForMissing} is true, in which
* case this situation results in a {@link TribbleException}
*/
public static Set addStandardFormatLines(final Set headerLines, final boolean throwErrorForMissing, final Collection IDs) {
return formatStandards.addToHeader(headerLines, IDs, throwErrorForMissing);
}
/**
* @see #addStandardFormatLines(java.util.Set, boolean, java.util.Collection)
*/
public static Set addStandardFormatLines(final Set headerLines, final boolean throwErrorForMissing, final String ... IDs) {
return addStandardFormatLines(headerLines, throwErrorForMissing, Arrays.asList(IDs));
}
/**
* Returns the standard format line for {@code ID}.
* If none exists, return null or throw an exception, depending on {@code throwErrorForMissing}.
*/
public static VCFFormatHeaderLine getFormatLine(final String ID, final boolean throwErrorForMissing) {
return formatStandards.get(ID, throwErrorForMissing);
}
/**
* Returns the standard format line for {@code ID}.
* If none exists, throw an {@link TribbleException}
*/
public static VCFFormatHeaderLine getFormatLine(final String ID) {
return formatStandards.get(ID, true);
}
/**
* Adds header lines for each of the info fields in {@code IDs} to header, returning the set of
* IDs without standard descriptions, unless {@code throwErrorForMissing} is true, in which
* case this situation results in a {@link TribbleException}.
*/
public static Set addStandardInfoLines(final Set headerLines, final boolean throwErrorForMissing, final Collection IDs) {
return infoStandards.addToHeader(headerLines, IDs, throwErrorForMissing);
}
/**
* @see #addStandardFormatLines(java.util.Set, boolean, java.util.Collection)
*/
public static Set addStandardInfoLines(final Set headerLines, final boolean throwErrorForMissing, final String ... IDs) {
return addStandardInfoLines(headerLines, throwErrorForMissing, Arrays.asList(IDs));
}
/**
* Returns the standard info line for {@code ID}.
* If none exists, return {@code null} or throw a {@link TribbleException}, depending on {@code throwErrorForMissing}.
*/
public static VCFInfoHeaderLine getInfoLine(final String ID, final boolean throwErrorForMissing) {
return infoStandards.get(ID, throwErrorForMissing);
}
/**
* Returns the standard info line for {@code ID}.
* If none exists throw a {@link TribbleException}.
*/
public static VCFInfoHeaderLine getInfoLine(final String ID) {
return getInfoLine(ID, true);
}
private static void registerStandard(final VCFInfoHeaderLine line) {
infoStandards.add(line);
}
private static void registerStandard(final VCFFormatHeaderLine line) {
formatStandards.add(line);
}
//
// VCF header line constants
//
static {
// FORMAT lines
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Integer, "Genotype Quality"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth (reads with MQ=255 or with bad mates are filtered)"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS, VCFHeaderLineCount.R, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Genotype-level filter"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.PHASE_SET_KEY, 1, VCFHeaderLineType.Integer, "Phasing set (typically the position of the first variant in the set)"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.PHASE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Read-backed phasing quality"));
// INFO lines
registerStandard(new VCFInfoHeaderLine(VCFConstants.END_KEY, 1, VCFHeaderLineType.Integer, "Stop position of the interval"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.DBSNP_KEY, 0, VCFHeaderLineType.Flag, "dbSNP Membership"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth; some reads may have been filtered"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.STRAND_BIAS_KEY, 1, VCFHeaderLineType.Float, "Strand Bias"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.MAPPING_QUALITY_ZERO_KEY, 1, VCFHeaderLineType.Integer, "Total Mapping Quality Zero Reads"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.RMS_MAPPING_QUALITY_KEY, 1, VCFHeaderLineType.Float, "RMS Mapping Quality"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.SOMATIC_KEY, 0, VCFHeaderLineType.Flag, "Somatic event"));
}
private static class Standards {
private final Map standards = new HashMap();
public T repair(final T line) {
final T standard = get(line.getID(), false);
if ( standard != null ) {
final boolean badCountType = line.getCountType() != standard.getCountType();
final boolean badCount = line.isFixedCount() && ! badCountType && line.getCount() != standard.getCount();
final boolean badType = line.getType() != standard.getType();
final boolean badDesc = ! line.getDescription().equals(standard.getDescription());
final boolean needsRepair = badCountType || badCount || badType || (REPAIR_BAD_DESCRIPTIONS && badDesc);
if ( needsRepair ) {
if ( GeneralUtils.DEBUG_MODE_ENABLED ) {
System.err.println("Repairing standard header line for field " + line.getID() + " because"
+ (badCountType ? " -- count types disagree; header has " + line.getCountType() + " but standard is " + standard.getCountType() : "")
+ (badType ? " -- type disagree; header has " + line.getType() + " but standard is " + standard.getType() : "")
+ (badCount ? " -- counts disagree; header has " + line.getCount() + " but standard is " + standard.getCount() : "")
+ (badDesc ? " -- descriptions disagree; header has '" + line.getDescription() + "' but standard is '" + standard.getDescription() + "'": ""));
}
return standard;
} else {
return line;
}
} else {
return line;
}
}
public Set addToHeader(final Set headerLines, final Collection IDs, final boolean throwErrorForMissing) {
final Set missing = new HashSet();
for ( final String ID : IDs ) {
final T line = get(ID, throwErrorForMissing);
if ( line == null )
missing.add(ID);
else
headerLines.add(line);
}
return missing;
}
public void add(final T line) {
if ( standards.containsKey(line.getID()) ) {
throw new TribbleException("Attempting to add multiple standard header lines for ID " + line.getID());
}
standards.put(line.getID(), line);
}
public T get(final String ID, final boolean throwErrorForMissing) {
final T x = standards.get(ID);
if ( throwErrorForMissing && x == null ) {
throw new TribbleException("Couldn't find a standard VCF header line for field " + ID);
}
return x;
}
}
}
