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gatk-3.8/public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java

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Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
/*
Updated all JAVA file licenses accordingly GSATDG-5
2013-01-11 06:04:08 +08:00
* 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.
*/
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
package org.broadinstitute.variant.vcf;
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
import org.broad.tribble.TribbleException;
org.broadinstitute.variant refactor, part 2 -removed sting dependencies from test classes -removed org.apache.log4j dependency -misc cleanup
2013-01-09 03:45:50 +08:00
import org.broadinstitute.variant.utils.GeneralUtils;
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
import java.util.*;
/**
* Manages header lines for standard VCF INFO and FORMAT fields
*
* Provides simple mechanisms for registering standard lines,
* looking them up, and 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<VCFFormatHeaderLine> formatStandards = new Standards<VCFFormatHeaderLine>();
private static Standards<VCFInfoHeaderLine> infoStandards = new Standards<VCFInfoHeaderLine>();
/**
* Walks over the VCF header and repairs the standard VCF header lines in it, returning a freshly
* allocated VCFHeader with standard VCF header lines repaired as necessary
*
* @param header
* @return
*/
@Requires("header != null")
@Ensures("result != null")
public static VCFHeader repairStandardHeaderLines(final VCFHeader header) {
Updates to VCF processing for better BCF processing -- getMetaData now split into getMetaDataInSortedOrder() [old functionality] and getMetaDataInOriginalOrder() [according to the header order]. Important as BCF uses the order of elements in the header in the offsets to keys, and we were automatically sorting the BCF2 header which is out of order in samtools and the whole system was going crazy -- Updating GATK code to use the appropriate header function (this is why so many files have changed) -- BCF2 code was busted in not differentiating PASS from . from FILTER in VC (tests coming that will actually stress this) -- Bugfix for adding contig lines to BCF2 header dictionary -- VCFHeader metaData no longer sorted internally. The system now maintains the data in header order, and only sorts output as requested in API -- VCFWriter and BCF2Writer now explictly sort their header lines -- Don't allow filters to be added that are PASS in the contract
2012-07-09 06:43:03 +08:00
final Set<VCFHeaderLine> newLines = new LinkedHashSet<VCFHeaderLine>(header.getMetaDataInInputOrder().size());
for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) {
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
if ( line instanceof VCFFormatHeaderLine ) {
line = formatStandards.repair((VCFFormatHeaderLine) line);
} else if ( line instanceof VCFInfoHeaderLine) {
line = infoStandards.repair((VCFInfoHeaderLine) line);
}
newLines.add(line);
}
return new VCFHeader(newLines, header.getGenotypeSamples());
}
/**
* Adds header lines for each of the format fields in IDs to header, returning the set of
* IDs without standard descriptions, unless throwErrorForMissing is true, in which
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
* case this situation results in a TribbleException
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
*
* @param IDs
* @return
*/
public static Set<String> addStandardFormatLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final Collection<String> IDs) {
return formatStandards.addToHeader(headerLines, IDs, throwErrorForMissing);
}
/**
* @see #addStandardFormatLines(java.util.Set, boolean, java.util.Collection)
*
* @param headerLines
* @param throwErrorForMissing
* @param IDs
* @return
*/
public static Set<String> addStandardFormatLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final String ... IDs) {
return addStandardFormatLines(headerLines, throwErrorForMissing, Arrays.asList(IDs));
}
/**
* Returns the standard format line for ID. If none exists, return null or throw an exception, depending
* on throwErrorForMissing
*
* @param ID
* @param throwErrorForMissing
* @return
*/
public static VCFFormatHeaderLine getFormatLine(final String ID, final boolean throwErrorForMissing) {
return formatStandards.get(ID, throwErrorForMissing);
}
/**
* Returns the standard format line for ID. If none exists throw an exception
*
* @param ID
* @return
*/
public static VCFFormatHeaderLine getFormatLine(final String ID) {
return formatStandards.get(ID, true);
}
private static void registerStandard(final VCFFormatHeaderLine line) {
formatStandards.add(line);
}
/**
* Adds header lines for each of the info fields in IDs to header, returning the set of
* IDs without standard descriptions, unless throwErrorForMissing is true, in which
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
* case this situation results in a TribbleException
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
*
* @param IDs
* @return
*/
public static Set<String> addStandardInfoLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final Collection<String> IDs) {
return infoStandards.addToHeader(headerLines, IDs, throwErrorForMissing);
}
/**
* @see #addStandardFormatLines(java.util.Set, boolean, java.util.Collection)
*
* @param IDs
* @return
*/
public static Set<String> addStandardInfoLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final String ... IDs) {
return addStandardInfoLines(headerLines, throwErrorForMissing, Arrays.asList(IDs));
}
/**
* Returns the standard info line for ID. If none exists, return null or throw an exception, depending
* on throwErrorForMissing
*
* @param ID
* @param throwErrorForMissing
* @return
*/
public static VCFInfoHeaderLine getInfoLine(final String ID, final boolean throwErrorForMissing) {
return infoStandards.get(ID, throwErrorForMissing);
}
/**
* Returns the standard info line for ID. If none exists throw an exception
*
* @param ID
* @return
*/
public static VCFInfoHeaderLine getInfoLine(final String ID) {
return getInfoLine(ID, true);
}
private static void registerStandard(final VCFInfoHeaderLine line) {
infoStandards.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.UNBOUNDED, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed"));
Genotype filters are now just Strings, not Set<String>
2012-06-29 02:27:09 +08:00
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, 1, VCFHeaderLineType.String, "Genotype-level filter"));
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
// INFO lines
registerStandard(new VCFInfoHeaderLine(VCFConstants.END_KEY, 1, VCFHeaderLineType.Integer, "Stop position of the interval"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.MLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.DOWNSAMPLED_KEY, 0, VCFHeaderLineType.Flag, "Were any of the samples downsampled?"));
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<T extends VCFCompoundHeaderLine> {
private final Map<String, T> standards = new HashMap<String, T>();
@Requires("line != null")
@Ensures({"result != null", "result.getID().equals(line.getID())"})
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 ) {
org.broadinstitute.variant refactor, part 2 -removed sting dependencies from test classes -removed org.apache.log4j dependency -misc cleanup
2013-01-09 03:45:50 +08:00
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() + "'": ""));
}
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
return standard;
} else
return line;
} else
return line;
}
@Requires("headerLines != null")
@Ensures({"result != null", "result.isEmpty() || ! throwErrorForMissing", "IDs.containsAll(result)"})
public Set<String> addToHeader(final Set<VCFHeaderLine> headerLines, final Collection<String> IDs, final boolean throwErrorForMissing) {
final Set<String> missing = new HashSet<String>();
for ( final String ID : IDs ) {
final T line = get(ID, throwErrorForMissing);
if ( line == null )
missing.add(ID);
else
headerLines.add(line);
}
return missing;
}
@Requires("line != null")
Bugfixes towards final BCF2 implementation -- MLAC and MLAF in PoolCaller now use standard MLE_AC and MLE_AF -- VCFDiffableReader disables onTheFly fixing of VCF header fields so comparisons are easier when headers are changing -- Flag fields with FLAG_KEY=0 are parsed as though FLAG_KEY were entirely absent in AbstractVCFCodec to fix bug where FLAG_KEY=0 was being translated into FLAG_KEY in output VCF, making a false flag value a true one -- Fix the GT field value in VariantContextTestProviders so it isn't fixed 1000s of times during testing -- Keys whose value is null are put into the VariantContext info attributes now
2012-06-21 08:00:17 +08:00
@Ensures({"standards.containsKey(line.getID())"})
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
public void add(final T line) {
if ( standards.containsKey(line.getID()) )
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
throw new TribbleException("Attempting to add multiple standard header lines for ID " + line.getID());
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
standards.put(line.getID(), line);
}
@Requires("ID != null")
@Ensures({"result != null || ! throwErrorForMissing"})
public T get(final String ID, final boolean throwErrorForMissing) {
final T x = standards.get(ID);
if ( throwErrorForMissing && x == null )
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
throw new TribbleException("Couldn't find a standard VCF header line for field " + ID);
Cleanup of VCF header lines and constants, BCF2 bugfixes -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header
2012-06-21 03:35:36 +08:00
return x;
}
}
}