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support for VCF4.5 just like (vcf4.4) . Changed optimistic_vcf_4_4 to optimistic_vcf_4_x #1751

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support for VCF4.5 just like (vcf4.4) . Changed optimistic_vcf_4_4 to optimistic_vcf_4_x #1751

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3a88518
change optimistic_vcf_4_4 to optimistic_vcf_4_x to support vcf4.4 and…
lindenb Dec 18, 2025
85f5da2
fix test for v4.x
lindenb Dec 18, 2025
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12 changes: 6 additions & 6 deletions build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -127,12 +127,12 @@ tasks.register('testWithDefaultReference', Test) {
}
}

tasks.register('testWithOptimisticVCF4_4', Test) {
tasks.register('testWithOptimisticVCF4_x', Test) {
description = "Run tests with optimistic VCF 4.4 reading"
jvmArgs += '-Dsamjdk.optimistic_vcf_4_4=true'
jvmArgs += '-Dsamjdk.optimistic_vcf_4_x=true'

useTestNG {
includeGroups "optimistic_vcf_4_4"
includeGroups "optimistic_vcf_4_x"
}
}

Expand All @@ -141,12 +141,12 @@ test {

useTestNG {
if (OperatingSystem.current().isUnix()) {
excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_4", "ftp", "http", "sra", "ena"
excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_x", "ftp", "http", "sra", "ena"
} else {
excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_4", "ftp", "http", "sra", "ena", "unix"
excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_x", "ftp", "http", "sra", "ena", "unix"
}
}
} dependsOn testWithDefaultReference, testWithOptimisticVCF4_4
} dependsOn testWithDefaultReference, testWithOptimisticVCF4_x


tasks.register('testFTP', Test) {
Expand Down
8 changes: 4 additions & 4 deletions src/main/java/htsjdk/samtools/Defaults.java
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Expand Up @@ -59,8 +59,8 @@ public class Defaults {
*/
public static final String DEFAULT_VCF_EXTENSION;

// accept VCF 4.4 files for read, but treat them as VCF 4.3
public static final boolean OPTIMISTIC_VCF_4_4;
// accept VCF 4.* files for read, but treat them as VCF 4.3
public static final boolean OPTIMISTIC_VCF_4_x;

/**
* Even if BUFFER_SIZE is 0, this is guaranteed to be non-zero. If BUFFER_SIZE is non-zero,
Expand Down Expand Up @@ -108,7 +108,7 @@ public class Defaults {
*/
public static final String DISABLE_SNAPPY_PROPERTY_NAME = "snappy.disable";

public static final String OPTIMISTIC_VCF_4_4_PROPERTY = "optimistic_vcf_4_4";
public static final String OPTIMISTIC_VCF_4_x_PROPERTY = "optimistic_vcf_4_x";


/**
Expand Down Expand Up @@ -139,7 +139,7 @@ public class Defaults {
SAM_FLAG_FIELD_FORMAT = SamFlagField.valueOf(getStringProperty("sam_flag_field_format", SamFlagField.DECIMAL.name()));
SRA_LIBRARIES_DOWNLOAD = getBooleanProperty("sra_libraries_download", false);
DISABLE_SNAPPY_COMPRESSOR = getBooleanProperty(DISABLE_SNAPPY_PROPERTY_NAME, false);
OPTIMISTIC_VCF_4_4 = getBooleanProperty(OPTIMISTIC_VCF_4_4_PROPERTY, false);
OPTIMISTIC_VCF_4_x = getBooleanProperty(OPTIMISTIC_VCF_4_x_PROPERTY, false);
}

/**
Expand Down
7 changes: 4 additions & 3 deletions src/main/java/htsjdk/variant/vcf/VCFCodec.java
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Expand Up @@ -100,12 +100,13 @@ public Object readActualHeader(final LineIterator lineIterator) {
throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");
foundHeaderVersion = true;
version = VCFHeaderVersion.toHeaderVersion(lineFields[1]);
if (Defaults.OPTIMISTIC_VCF_4_4 == true && version == VCFHeaderVersion.VCF4_4 ) {
if (Defaults.OPTIMISTIC_VCF_4_x == true && (version == VCFHeaderVersion.VCF4_4 || version == VCFHeaderVersion.VCF4_5)) {
// if optimistic VCFv4.4 is enabled, accept VCFv4.4 as input, but treat it as VCFv4.3, and hope for the best
log.warn("********** VCFv4.4 is not yet fully supported - processing VCFv4.4 input as VCFv4.3! **********");
log.warn("********** versions >=VCFv4.4 are not yet fully supported - processing >=VCFv4.4 input as VCFv4.3! **********");
version = VCFHeaderVersion.VCF4_3;
} else if ( version != VCFHeaderVersion.VCF4_0 && version != VCFHeaderVersion.VCF4_1 && version != VCFHeaderVersion.VCF4_2 && version != VCFHeaderVersion.VCF4_3)
throw new TribbleException.InvalidHeader("This codec is strictly for VCFv4 and does not support " + lineFields[1]);
throw new TribbleException.InvalidHeader("This codec is strictly for VCFv4 and does not support " + lineFields[1]+" . "
+ "For Versions >= VCF4.4 you can try to set the java property -D" + Defaults.SAMJDK_PREFIX + Defaults.OPTIMISTIC_VCF_4_x_PROPERTY + "=true");
}
headerStrings.add(lineIterator.next());
}
Expand Down
7 changes: 4 additions & 3 deletions src/main/java/htsjdk/variant/vcf/VCFHeaderVersion.java
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Expand Up @@ -38,9 +38,10 @@ public enum VCFHeaderVersion {
VCF4_1("VCFv4.1", "fileformat"),
VCF4_2("VCFv4.2", "fileformat"),
VCF4_3("VCFv4.3", "fileformat"),
// VCFv4.4 is not fully supported yet, but we need this to support optimistic reading when
// the "optimistic_vcf_4_4" property is set
VCF4_4("VCFv4.4", "fileformat");
// VCFv4.4 and VCFv4.5 are not fully supported yet, but we need this to support optimistic reading when
// the "optimistic_vcf_4_x" property is set
VCF4_4("VCFv4.4", "fileformat"),
VCF4_5("VCFv4.5", "fileformat");

private final String versionString;
private final String formatString;
Expand Down
13 changes: 11 additions & 2 deletions src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
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Expand Up @@ -100,7 +100,7 @@ public void testBlockCompressionExtension(final String testURIString, final bool
public void testBlockCompressionExtensionStringVersion(final String testURIString, final boolean expected) {
Assert.assertEquals(AbstractFeatureReader.hasBlockCompressedExtension(testURIString), expected);
}
@Test(groups = "optimistic_vcf_4_4")
@Test(groups = "optimistic_vcf_4_x")
public void testVCF4_4Optimistic() {
final AbstractFeatureReader<VariantContext, ?> fr = AbstractFeatureReader.getFeatureReader(
Paths.get("src/test/resources/htsjdk/variant/", "VCF4_4HeaderTest.vcf").toString(),
Expand All @@ -109,7 +109,16 @@ public void testVCF4_4Optimistic() {
final VCFHeader vcfHeader = (VCFHeader) fr.getHeader();
Assert.assertEquals(vcfHeader.getVCFHeaderVersion(), VCFHeaderVersion.VCF4_3);
}

@Test(groups = "optimistic_vcf_4_x")
public void testVCF4_5Optimistic() {
final AbstractFeatureReader<VariantContext, ?> fr = AbstractFeatureReader.getFeatureReader(
Paths.get("src/test/resources/htsjdk/variant/", "VCF4_5HeaderTest.vcf").toString(),
new VCFCodec(),
false);
final VCFHeader vcfHeader = (VCFHeader) fr.getHeader();
Assert.assertEquals(vcfHeader.getVCFHeaderVersion(), VCFHeaderVersion.VCF4_3);
}

@DataProvider(name = "vcfFileAndWrapperCombinations")
private static Object[][] vcfFileAndWrapperCombinations(){
return new Object[][] {
Expand Down
42 changes: 42 additions & 0 deletions src/test/resources/htsjdk/variant/VCF4_5HeaderTest.vcf
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@@ -0,0 +1,42 @@
##fileformat=VCFv4.5
##FILTER=<ID=ABFilter,Description="AB 0.75 && DP 40">
##FILTER=<ID=DPFilter,Description="DP 120 || SB -0.10">
##FILTER=<ID=FDRtranche0.00to0.10,Description="FDR tranche level at qual 0.06">
##FILTER=<ID=FDRtranche0.10to1.00,Description="FDR tranche level at qual 0.03">
##FILTER=<ID=FDRtranche1.00to2.00,Description="FDR tranche level at qual 0.02">
##FILTER=<ID=FDRtranche2.00to10.00+,Description="FDR tranche level at qual > 0.06">
##FILTER=<ID=FDRtranche2.00to10.00,Description="FDR tranche level at qual unknown">
##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 = 4 && ((MQ0 / (1.0 * DP)) 0.1)">
##FILTER=<ID=Indel,Description="Overlaps a user-input mask">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=LowQual,Description="QUAL 50.0">
##FILTER=<ID=ANNOTATION,Description="ANNOTATION != \"NA\" || ANNOTATION <= 0.01">
##FILTER=<ID=ANNOTATION2,Description="ANNOTATION with quote \" that is unmatched but escaped">
##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
##INFO=<ID=EscapingQuote,Number=1,Type=Float,Description="This description has an escaped \" quote in it">
##INFO=<ID=EscapingBackslash,Number=1,Type=Float,Description="This description has an escaped \\ backslash in it">
##INFO=<ID=EscapingNonQuoteOrBackslash,Number=1,Type=Float,Description="This other value has a \n newline in it">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=OQ,Number=1,Type=Float,Description="The original variant quality score">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-23/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-24/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-5/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-9/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-6/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-19/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-25/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-4/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-14/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-22/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-2/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-3/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-7/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-16/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-1/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-17/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-8/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-10/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-18/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-20/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-11/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-15/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-21/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-12/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-13/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam] read_buffer_size=null read_filter=[] intervals=[chrX] excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod, interval,Intervals,chrX] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod hapmap=null hapmap_chip=null out=null err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=10000 num_threads=1 interval_merging=ALL read_group_black_list=null genotype_model=JOINT_ESTIMATE base_model=EMPIRICAL heterozygosity=7.8E-4 genotype=false output_all_callable_bases=false standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 trigger_min_confidence_threshold_for_calling=30.0 trigger_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=null platform=null min_base_quality_score=20 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.05 cap_base_quality_by_mapping_quality=false"
##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null read_filter=[] intervals=null excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[variant,VCF,wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.vcf, mask,Bed,wgs.v9/HiSeq.WGS.cleaned.indels.10.mask] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=2147483647 num_threads=1 interval_merging=ALL read_group_black_list=null filterExpression=[] filterName=[] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Indel NO_HEADER=false"
##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null read_filter=[] intervals=null excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[variant,VCF,wgs.v9/HiSeq.WGS.cleaned.ug.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.vcf err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=2147483647 num_threads=1 interval_merging=ALL read_group_black_list=null filterExpression=[QUAL < 50.0, MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1), AB > 0.75 && DP > 40, DP > 120 || SB > -0.10] filterName=[LowQual, HARD_TO_VALIDATE, ABFilter, DPFilter] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=10 maskName=Mask NO_HEADER=false"
##source=VariantOptimizer
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr1 109 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1019;Dels=0.00;HRun=0;HaplotypeScore=686.65;MQ=19.20;MQ0=288;OQ=2175.54;QD=2.13;SB=-1042.18 GT:AD:DP:GL:GQ 0/1:610,327:308:-316.30,-95.47,-803.03:99
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