de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions Maven / Gradle / Ivy
package de.charite.compbio.jannovar.cmd.annotate_vcf;
import de.charite.compbio.jannovar.UncheckedJannovarException;
import de.charite.compbio.jannovar.cmd.CommandLineParsingException;
import de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions;
import de.charite.compbio.jannovar.cmd.JannovarBaseOptions;
import de.charite.compbio.jannovar.filter.facade.PedigreeFilterOptions;
import de.charite.compbio.jannovar.filter.facade.ThresholdFilterOptions;
import de.charite.compbio.jannovar.vardbs.generic_tsv.GenericTSVAnnotationOptions;
import de.charite.compbio.jannovar.vardbs.generic_vcf.GenericVCFAnnotationOptions;
import java.util.ArrayList;
import java.util.List;
import java.util.function.BiFunction;
import net.sourceforge.argparse4j.impl.Arguments;
import net.sourceforge.argparse4j.inf.ArgumentGroup;
import net.sourceforge.argparse4j.inf.ArgumentParser;
import net.sourceforge.argparse4j.inf.Namespace;
import net.sourceforge.argparse4j.inf.Subparser;
import net.sourceforge.argparse4j.inf.Subparsers;
/**
* Options for annotating VCF files
*
* @author Manuel Holtgrewe
*/
public class JannovarAnnotateVCFOptions extends JannovarAnnotationOptions {
/** Whether or not to escape ANN field */
private boolean escapeAnnField = true;
/** Path to input VCF file */
private String pathInputVCF = null;
/** Interval to annotate */
private String interval = "";
/** Path to output VCF file */
private String pathOutputVCF = null;
/** Path to dbSNP VCF file to use for the annotation */
public String pathVCFDBSNP = null;
/** Prefix to use for dbSNP VCF INFO Fields */
public String prefixDBSNP = null;
/**
* Path to the reference FAI-indexed FASTA file (required for dbSNP/ExAC/UK10K-based annotation
*/
public String pathFASTARef = null;
/** Path to ExAC VCF file to use for the annotation */
public String pathVCFExac;
/** Prefix to use for ExAC VCF INFO Fields */
public String prefixExac;
/** Path to gnomAD exomes VCF file to use for the annotation */
public String pathVCFGnomadExomes;
/** Prefix to use for gnomAD exomes INFO fields */
public String prefixGnomadExomes;
/** Path to gnomAD genomes VCF file to use for the annotation */
public String pathVCFGnomadGenomes;
/** Prefix to use for gnomAD genomes INFO fields */
public String prefixGnomadGenomes;
/** Path to UK10K VCF file to use for the annotation */
public String pathVCFUK10K;
/** Prefix to use for UK10K VCF INFO Fields */
public String prefixUK10K;
/** Path to ClinVar VCF file to use for the annotation */
public String pathClinVar;
/** Prefix to use for ClinVar VCF INFO Fields */
public String prefixClinVar;
/** Path to COSMIC VCF file to use for the annotation */
public String pathCosmic;
/** Prefix to use for COSMIC VCF INFO Fields */
public String prefixCosmic;
/** Path to pedigree file */
public String pathPedFile;
/**
* Whether or not to perform compatible inheritance mode annotation with the assumption that the
* single individual is the affected index.
*/
public boolean annotateAsSingletonPedigree;
/** Whether or not to use threshold-based filters */
public boolean useThresholdFilters;
/**
* Whether or not to use the advanced pedigree filters (mainly useful for de novo variants)
*/
public boolean useAdvancedPedigreeFilters;
/** Threshold filter: minimal coverage at a site for heterozygous calls */
private int threshFiltMinGtCovHet;
/** Threshold filter: minimal coverage at a site for homozygous calls */
private int threshFiltMinGtCovHomAlt;
/** Threshold filter: maximal coverage at a site for any call */
private int threshFiltMaxCov;
/** Threshold filter: minimal genotype for calls */
private int threshFiltMinGtGq;
/**
* Threshold filter: minimal alternative allele fraction for heterozygous calls
*/
private double threshFiltMinGtAafHet;
/**
* Threshold filter: maximal alternative allele fraction for heterozygous calls
*/
private double threshFiltMaxGtAafHet;
/**
* Threshold filter: minimal alternative allele fraction for homozygous alternative calls
*/
private double threshFiltMinGtAafHomAlt;
/**
* Threshold filter: maximal alternative allele fraction for homozygous ref calls
*/
private double threshFiltMaxGtAafHomRef;
/**
* Threshold filter: maximal allele frequency for autosomal dominant inheritance mode
*/
private double threshFiltMaxAlleleFrequencyAd;
/**
* Threshold filter: maximal allele frequency for autosomal recessive inheritance mode
*/
private double threshFiltMaxAlleleFrequencyAr;
/** Enable off target filter */
private boolean offTargetFilterEnabled;
/** Count UTR as off-target */
private boolean offTargetFilterUtrIsOffTarget;
/** Count intronic splice region (non-consensus) as off-target */
private boolean offTargetFilterIntronicSpliceIsOffTarget;
/**
* Whether or not to use the variant-wise (AllAffGtFiltered, MaxFreqAd, MaxFreqAr, and OffExome)
* and genotype-wise filters (MaxCov, MinCovHet, MinCovHomAlt, MinGq, MinAafHet, MaxAafHet,
* MinAafHomAlt, MinAafHomRef) in inheritance mode compatibility annotation.
*/
private boolean inheritanceAnnoUseFilters;
/** Whether or not to enable the "parent GT is filtered" GT filter, default is true. */
private boolean useParentGtIsFiltered;
/** Maximal support of alternative allele in parent for de novo variant. */
private Integer threshDeNovoParentAd2;
/** Configuration for annotation with BED files. */
private List bedAnnotationOptions = new ArrayList<>();
/** Column of contig name in dbNSFP. */
private int dbNsfpColContig;
/** Column of contig name in dbNSFP. */
private int dbNsfpColPosition;
/** Prefix for dbNSFP annotations. */
private String prefixDbNsfp;
/** Configuration for annotation with dbNSFP. */
private String pathDbNsfp;
/** Fields to annotate with from dbNSFP. */
private List columnsDbNsfp = new ArrayList<>();
/** Configuration for annotation with generic TSV files. */
private List tsvAnnotationOptions = new ArrayList<>();
/** Configuration for annotation with VCF files. */
private List vcfAnnotationOptions = new ArrayList<>();
/**
* Setup {@link ArgumentParser}
*
* @param subParsers {@link Subparsers} to setup
*/
public static void setupParser(Subparsers subParsers) {
BiFunction handler = (argv, args) -> {
try {
return new AnnotateVCFCommand(argv, args);
} catch (CommandLineParsingException e) {
throw new UncheckedJannovarException("Could not parse command line", e);
}
};
Subparser subParser = subParsers.addParser("annotate-vcf", true).help("annotate VCF files")
.setDefault("cmd", handler);
subParser.description("Perform annotation of a single VCF file");
ArgumentGroup requiredGroup = subParser.addArgumentGroup("Required arguments");
requiredGroup.addArgument("-i", "--input-vcf").help("Path to input VCF file")
.required(true);
requiredGroup.addArgument("-o", "--output-vcf").help("Path to output VCF file")
.required(true);
requiredGroup.addArgument("-d", "--database").help("Path to database .ser file")
.required(true);
ArgumentGroup annotationGroup =
subParser.addArgumentGroup("Annotation Arguments (optional)");
requiredGroup.addArgument("--interval").help("Interval with regions to annotate (optional)")
.required(false).setDefault("");
annotationGroup.addArgument("--pedigree-file")
.help("Pedigree file to use for Mendelian inheritance annotation").required(false);
annotationGroup.addArgument("--annotate-as-singleton-pedigree")
.help("Annotate VCF file with single individual as singleton pedigree (singleton assumed to be affected)")
.required(false).setDefault(false).action(Arguments.storeTrue());
annotationGroup.addArgument("--ref-fasta").help(
"Path to FAI-indexed reference FASTA file, required for dbSNP/ExAC/UK10K-based annotation");
annotationGroup.addArgument("--dbsnp-vcf")
.help("Path to dbSNP VCF file, activates dbSNP annotation").required(false);
annotationGroup.addArgument("--dbsnp-prefix").help("Prefix for dbSNP annotations")
.setDefault("DBSNP_").required(false);
annotationGroup.addArgument("--exac-vcf")
.help("Path to ExAC VCF file, activates ExAC annotation").required(false);
annotationGroup.addArgument("--exac-prefix").help("Prefix for ExAC annotations")
.setDefault("EXAC_").required(false);
annotationGroup.addArgument("--gnomad-exomes-vcf")
.help("Path to gnomAD exomes VCF file, activates gnomAD exomes annotation")
.required(false);
annotationGroup.addArgument("--gnomad-exomes-prefix")
.help("Prefix for ExgnomAD exomes AC annotations").setDefault("GNOMAD_EXOMES_")
.required(false);
annotationGroup.addArgument("--gnomad-genomes-vcf")
.help("Path to gnomAD genomes VCF file, activates gnomAD genomes annotation")
.required(false);
annotationGroup.addArgument("--gnomad-genomes-prefix")
.help("Prefix for ExgnomAD genomes AC annotations").setDefault("GNOMAD_GENOMES_")
.required(false);
annotationGroup.addArgument("--uk10k-vcf")
.help("Path to UK10K VCF file, activates UK10K annotation").required(false);
annotationGroup.addArgument("--uk10k-prefix").help("Prefix for UK10K annotations")
.setDefault("UK10K_").required(false);
annotationGroup.addArgument("--clinvar-vcf")
.help("Path to ClinVar file, activates ClinVar annotation").required(false);
annotationGroup.addArgument("--clinvar-prefix").help("Prefix for ClinVar annotations")
.setDefault("CLINVAR_").required(false);
annotationGroup.addArgument("--cosmic-vcf")
.help("Path to COSMIC file, activates COSMIC annotation").required(false);
annotationGroup.addArgument("--cosmic-prefix").help("Prefix for COSMIC annotations")
.setDefault("COSMIC_").required(false);
annotationGroup.addArgument("--inheritance-anno-use-filters")
.help("Use filters in inheritance mode annotation").setDefault(false)
.action(Arguments.storeTrue());
ArgumentGroup dbNsfpAnnotationGroup =
subParser.addArgumentGroup("Annotation with dbNSFP (experimental; optional)");
dbNsfpAnnotationGroup.addArgument("--dbnsfp-tsv").help("Patht to dbNSFP TSV file")
.required(false);
dbNsfpAnnotationGroup.addArgument("--dbnsfp-col-contig").type(Integer.class)
.help("Column index of contig in dbNSFP").setDefault(1);
dbNsfpAnnotationGroup.addArgument("--dbnsfp-col-position").type(Integer.class)
.help("Column index of position in dbNSFP").setDefault(2);
dbNsfpAnnotationGroup.addArgument("--dbnsfp-prefix").help("Prefix for dbNSFP annotations")
.setDefault("DBNSFP_").required(false);
dbNsfpAnnotationGroup.addArgument("--dbnsfp-columns")
.help("Columns from dbDSFP file to use for annotation").action(Arguments.append());
ArgumentGroup bedAnnotationGroup =
subParser.addArgumentGroup("BED-based Annotation (experimental; optional)");
bedAnnotationGroup.addArgument("--bed-annotation")
.help("Add BED file to use for annotating. The value must be of the format "
+ "\"pathToBed:infoField:description[:colNo]\".")
.action(Arguments.append());
ArgumentGroup vcfAnnotationGroup =
subParser.addArgumentGroup("Generic VCF-based Annotation (experimental; optional)");
vcfAnnotationGroup.addArgument("--vcf-annotation")
.help("Add VCF file to use for annotating. The value must be of the format "
+ "\"pathToVfFile:prefix:field1,field2,field3\".")
.action(Arguments.append());
ArgumentGroup tsvAnnotationGroup =
subParser.addArgumentGroup("TSV-based Annotation (experimental; optional)");
tsvAnnotationGroup.addArgument("--tsv-annotation")
.help("Add TSV file to use for annotating. The value must be of the format "
+ "\"pathToTsvFile:oneBasedOffset:colContig:colStart:colEnd:colRef(or=0):"
+ "colAlt(or=0):isRefAnnotated(R=yes,A=no):colValue:fieldType:fieldName:fieldDescription:"
+ "accumulationStrategy\".")
.action(Arguments.append());
ArgumentGroup threshFilterGroup =
subParser.addArgumentGroup("Threshold-filter related arguments");
threshFilterGroup.addArgument("--use-threshold-filters").help("Use threshold-based filters")
.setDefault(false).action(Arguments.storeTrue());
ThresholdFilterOptions threshDefaults = ThresholdFilterOptions.buildDefaultOptions();
threshFilterGroup.addArgument("--gt-thresh-filt-min-cov-het")
.help("Minimal coverage for het. call").setDefault(threshDefaults.getMinGtCovHet())
.type(Integer.class);
threshFilterGroup.addArgument("--gt-thresh-filt-min-cov-hom-alt")
.help("Minimal coverage for hom. alt calls")
.setDefault(threshDefaults.getMinGtCovHomAlt()).type(Integer.class);
threshFilterGroup.addArgument("--gt-thresh-filt-max-cov")
.help("Maximal coverage for a sample").setDefault(threshDefaults.getMaxCov())
.type(Integer.class);
threshFilterGroup.addArgument("--gt-thresh-filt-min-gq")
.help("Minimal genotype call quality").setDefault(threshDefaults.getMinGtGq())
.type(Integer.class);
threshFilterGroup.addArgument("--gt-thresh-filt-min-aaf-het")
.help("Minimal het. call alternate allele fraction")
.setDefault(threshDefaults.getMinGtAafHet()).type(Double.class);
threshFilterGroup.addArgument("--gt-thresh-filt-max-aaf-het")
.help("Maximal het. call alternate allele fraction")
.setDefault(threshDefaults.getMaxGtAafHet()).type(Double.class);
threshFilterGroup.addArgument("--gt-thresh-filt-min-aaf-hom-alt")
.help("Minimal hom. alt call alternate allele fraction")
.setDefault(threshDefaults.getMinGtAafHomAlt()).type(Double.class);
threshFilterGroup.addArgument("--gt-thresh-filt-max-aaf-hom-ref")
.help("Maximal hom. ref call alternate allele fraction")
.setDefault(threshDefaults.getMaxGtAafHomRef()).type(Double.class);
threshFilterGroup.addArgument("--var-thresh-max-allele-freq-ad")
.help("Maximal allele fraction for autosomal dominant inheritance mode")
.setDefault(threshDefaults.getMaxAlleleFrequencyAd()).type(Double.class);
threshFilterGroup.addArgument("--var-thresh-max-allele-freq-ar")
.help("Maximal allele fraction for autosomal recessive inheritance mode")
.setDefault(threshDefaults.getMaxAlleleFrequencyAr()).type(Double.class);
PedigreeFilterOptions pedDefaults = PedigreeFilterOptions.buildDefaultOptions();
threshFilterGroup.addArgument("--use-advanced-pedigree-filters")
.help("Use advanced pedigree-based filters (mainly useful for de novo variants)")
.setDefault(false).action(Arguments.storeTrue());
threshFilterGroup.addArgument("--de-novo-max-parent-ad2")
.help("Maximal support of alternative allele in parent for de novo variants.")
.type(Integer.class).setDefault(pedDefaults.getDeNovoMaxParentAd2());
ArgumentGroup offTargetGroup = subParser.addArgumentGroup("Exome on/off target filters");
offTargetGroup.addArgument("--enable-off-target-filter")
.help("Enable filter for on/off-target based on effect impact").setDefault(false)
.action(Arguments.storeTrue());
offTargetGroup.addArgument("--utr-is-off-target")
.help("Make UTR count as off-target (default is to count UTR as on-target)")
.setDefault(false).action(Arguments.storeTrue());
offTargetGroup.addArgument("--intronic-splice-is-off-target")
.help("Make intronic (non-consensus site) splice region count as off-target (default is to count as on-target)")
.setDefault(false).action(Arguments.storeTrue());
ArgumentGroup optionalGroup = subParser.addArgumentGroup("Other, optional Arguments");
optionalGroup.addArgument("--no-escape-ann-field")
.help("Disable escaping of INFO/ANN field in VCF output").dest("escape_ann_field")
.setDefault(true).action(Arguments.storeFalse());
optionalGroup.addArgument("--show-all").help("Show all effects").setDefault(false)
.action(Arguments.storeTrue());
optionalGroup.addArgument("--no-3-prime-shifting")
.help("Disable shifting towards 3' of transcript").dest("3_prime_shifting")
.setDefault(true).action(Arguments.storeFalse());
optionalGroup.addArgument("--3-letter-amino-acids")
.help("Enable usage of 3 letter amino acid codes").setDefault(false)
.action(Arguments.storeTrue());
optionalGroup.addArgument("--disable-parent-gt-is-filtered").setDefault(true)
.dest("use_parent_gt_is_filtered").action(Arguments.storeFalse());
JannovarBaseOptions.setupParser(subParser);
}
@Override
public void setFromArgs(Namespace args) throws CommandLineParsingException {
super.setFromArgs(args);
interval = args.getString("interval");
escapeAnnField = args.getBoolean("escape_ann_field");
pathInputVCF = args.getString("input_vcf");
pathOutputVCF = args.getString("output_vcf");
pathPedFile = args.getString("pedigree_file");
annotateAsSingletonPedigree = args.getBoolean("annotate_as_singleton_pedigree");
pathFASTARef = args.getString("ref_fasta");
pathVCFDBSNP = args.getString("dbsnp_vcf");
prefixDBSNP = args.getString("dbsnp_prefix");
pathVCFExac = args.getString("exac_vcf");
prefixExac = args.getString("exac_prefix");
pathVCFGnomadExomes = args.getString("gnomad_exomes_vcf");
prefixGnomadExomes = args.getString("gnomad_exomes_prefix");
pathVCFGnomadGenomes = args.getString("gnomad_genomes_vcf");
prefixGnomadGenomes = args.getString("gnomad_genomes_prefix");
pathVCFUK10K = args.getString("uk10k_vcf");
prefixUK10K = args.getString("uk10k_prefix");
pathClinVar = args.getString("clinvar_vcf");
prefixClinVar = args.getString("clinvar_prefix");
pathCosmic = args.getString("cosmic_vcf");
prefixCosmic = args.getString("cosmic_prefix");
inheritanceAnnoUseFilters = args.getBoolean("inheritance_anno_use_filters");
useParentGtIsFiltered = args.getBoolean("use_parent_gt_is_filtered");
dbNsfpColContig = args.getInt("dbnsfp_col_contig");
dbNsfpColPosition = args.getInt("dbnsfp_col_position");
prefixDbNsfp = args.getString("dbnsfp_prefix");
pathDbNsfp = args.getString("dbnsfp_tsv");
if (args.getList("dbnsfp_columns") != null) {
for (Object o : args.getList("dbnsfp_columns")) {
final String s = (String) o;
for (String s2 : s.split(",")) {
if (!DbNsfpFields.DBNSFP_FIELDS.containsKey(s2)) {
throw new RuntimeException(
"Unknown field from dbNSFP or not yet supported: " + s);
} else {
columnsDbNsfp.add(s2);
}
}
}
}
if (args.getList("bed_annotation") != null) {
for (Object o : args.getList("bed_annotation")) {
final String s = (String) o;
bedAnnotationOptions.add(BedAnnotationOptions.parseFrom(s));
}
}
if (args.getList("tsv_annotation") != null) {
for (Object o : args.getList("tsv_annotation")) {
final String s = (String) o;
tsvAnnotationOptions.add(GenericTSVAnnotationOptions.parseFrom(s));
}
}
if (args.getList("vcf_annotation") != null) {
for (Object o : args.getList("vcf_annotation")) {
final String s = (String) o;
vcfAnnotationOptions.add(GenericVCFAnnotationOptions.parseFrom(s));
}
}
useThresholdFilters = args.getBoolean("use_threshold_filters");
threshFiltMinGtCovHet = args.getInt("gt_thresh_filt_min_cov_het");
threshFiltMinGtCovHomAlt = args.getInt("gt_thresh_filt_min_cov_hom_alt");
threshFiltMaxCov = args.getInt("gt_thresh_filt_max_cov");
threshFiltMinGtGq = args.getInt("gt_thresh_filt_min_gq");
threshFiltMinGtAafHet = args.getDouble("gt_thresh_filt_min_aaf_het");
threshFiltMaxGtAafHet = args.getDouble("gt_thresh_filt_max_aaf_het");
threshFiltMinGtAafHomAlt = args.getDouble("gt_thresh_filt_min_aaf_hom_alt");
threshFiltMaxGtAafHomRef = args.getDouble("gt_thresh_filt_max_aaf_hom_ref");
threshFiltMaxAlleleFrequencyAd = args.getDouble("var_thresh_max_allele_freq_ad");
threshFiltMaxAlleleFrequencyAr = args.getDouble("var_thresh_max_allele_freq_ar");
useAdvancedPedigreeFilters = args.getBoolean("use_advanced_pedigree_filters");
setThreshDeNovoParentAd2(args.getInt("de_novo_max_parent_ad2"));
offTargetFilterEnabled = args.getBoolean("enable_off_target_filter");
offTargetFilterUtrIsOffTarget = args.getBoolean("utr_is_off_target");
offTargetFilterIntronicSpliceIsOffTarget = args.getBoolean("intronic_splice_is_off_target");
if (pathFASTARef == null && (pathVCFDBSNP != null || pathVCFExac != null
|| pathVCFUK10K != null || pathClinVar != null || pathCosmic != null
|| pathVCFGnomadExomes != null || pathVCFGnomadGenomes != null || pathDbNsfp != null
|| !tsvAnnotationOptions.isEmpty() || !vcfAnnotationOptions.isEmpty()))
throw new CommandLineParsingException(
"Command --ref-fasta required when using dbSNP, ExAC, UK10K, ClinVar, or COSMIC annotations.");
}
public String getInterval() {
return interval;
}
public void setInterval(String interval) {
this.interval = interval;
}
public String getPathInputVCF() {
return pathInputVCF;
}
public void setPathInputVCF(String pathInputVCF) {
this.pathInputVCF = pathInputVCF;
}
public String getPathOutputVCF() {
return pathOutputVCF;
}
public void setPathOutputVCF(String pathOutputVCF) {
this.pathOutputVCF = pathOutputVCF;
}
public boolean isEscapeAnnField() {
return escapeAnnField;
}
public void setEscapeAnnField(boolean escapeAnnField) {
this.escapeAnnField = escapeAnnField;
}
public String getPathVCFDBSNP() {
return pathVCFDBSNP;
}
public void setPathVCFDBSNP(String pathVCFDBSNP) {
this.pathVCFDBSNP = pathVCFDBSNP;
}
public String getPrefixDBSNP() {
return prefixDBSNP;
}
public void setPrefixDBSNP(String prefixDBSNP) {
this.prefixDBSNP = prefixDBSNP;
}
public String getPathFASTARef() {
return pathFASTARef;
}
public void setPathFASTARef(String pathFASTARef) {
this.pathFASTARef = pathFASTARef;
}
public String getPathVCFExac() {
return pathVCFExac;
}
public void setPathVCFExac(String pathVCFExac) {
this.pathVCFExac = pathVCFExac;
}
public String getPrefixExac() {
return prefixExac;
}
public void setPrefixExac(String prefixExac) {
this.prefixExac = prefixExac;
}
public String getPathVCFUK10K() {
return pathVCFUK10K;
}
public void setPathVCFUK10K(String pathVCFUK10K) {
this.pathVCFUK10K = pathVCFUK10K;
}
public String getPrefixUK10K() {
return prefixUK10K;
}
public void setPrefixUK10K(String prefixUK10K) {
this.prefixUK10K = prefixUK10K;
}
public String getPathClinVar() {
return pathClinVar;
}
public void setPathClinVar(String pathClinVar) {
this.pathClinVar = pathClinVar;
}
public String getPrefixClinVar() {
return prefixClinVar;
}
public void setPrefixClinVar(String prefixClinVar) {
this.prefixClinVar = prefixClinVar;
}
public String getPathCosmic() {
return pathCosmic;
}
public void setPathCosmic(String pathCosmic) {
this.pathCosmic = pathCosmic;
}
public String getPrefixCosmic() {
return prefixCosmic;
}
public void setPrefixCosmic(String prefixCosmic) {
this.prefixCosmic = prefixCosmic;
}
public String getPathVCFGnomadExomes() {
return pathVCFGnomadExomes;
}
public void setPathVCFGnomadExomes(String pathVCFGnomadExomes) {
this.pathVCFGnomadExomes = pathVCFGnomadExomes;
}
public String getPrefixGnomadExomes() {
return prefixGnomadExomes;
}
public void setPrefixGnomadExomes(String prefixGnomadExomes) {
this.prefixGnomadExomes = prefixGnomadExomes;
}
public String getPathVCFGnomadGenomes() {
return pathVCFGnomadGenomes;
}
public void setPathVCFGnomadGenomes(String pathVCFGnomadGenomes) {
this.pathVCFGnomadGenomes = pathVCFGnomadGenomes;
}
public String getPrefixGnomadGenomes() {
return prefixGnomadGenomes;
}
public void setPrefixGnomadGenomes(String prefixGnomadGenomes) {
this.prefixGnomadGenomes = prefixGnomadGenomes;
}
public boolean isAnnotateAsSingletonPedigree() {
return annotateAsSingletonPedigree;
}
public void setAnnotateAsSingletonPedigree(boolean annotateAsSingletonPedigree) {
this.annotateAsSingletonPedigree = annotateAsSingletonPedigree;
}
public String getPathPedFile() {
return pathPedFile;
}
public void setPathPedFile(String pathPedFile) {
this.pathPedFile = pathPedFile;
}
public boolean isUseThresholdFilters() {
return useThresholdFilters;
}
public void setUseThresholdFilters(boolean useThresholdFilters) {
this.useThresholdFilters = useThresholdFilters;
}
public int getThreshFiltMinGtCovHet() {
return threshFiltMinGtCovHet;
}
public void setThreshFiltMinGtCovHet(int threshFiltMinGtCovHet) {
this.threshFiltMinGtCovHet = threshFiltMinGtCovHet;
}
public int getThreshFiltMinGtCovHomAlt() {
return threshFiltMinGtCovHomAlt;
}
public void setThreshFiltMinGtCovHomAlt(int threshFiltMinGtCovHomAlt) {
this.threshFiltMinGtCovHomAlt = threshFiltMinGtCovHomAlt;
}
public int getThreshFiltMaxCov() {
return threshFiltMaxCov;
}
public void setThreshFiltMaxCov(int threshFiltMaxCov) {
this.threshFiltMaxCov = threshFiltMaxCov;
}
public int getThreshFiltMinGtGq() {
return threshFiltMinGtGq;
}
public void setThreshFiltMinGtGq(int threshFiltMinGtGq) {
this.threshFiltMinGtGq = threshFiltMinGtGq;
}
public double getThreshFiltMinGtAafHet() {
return threshFiltMinGtAafHet;
}
public void setThreshFiltMinGtAafHet(double threshFiltMinGtAafHet) {
this.threshFiltMinGtAafHet = threshFiltMinGtAafHet;
}
public double getThreshFiltMaxGtAafHet() {
return threshFiltMaxGtAafHet;
}
public void setThreshFiltMaxGtAafHet(double threshFiltMaxGtAafHet) {
this.threshFiltMaxGtAafHet = threshFiltMaxGtAafHet;
}
public double getThreshFiltMinGtAafHomAlt() {
return threshFiltMinGtAafHomAlt;
}
public void setThreshFiltMinGtAafHomAlt(double threshFiltMinGtAafHomAlt) {
this.threshFiltMinGtAafHomAlt = threshFiltMinGtAafHomAlt;
}
public double getThreshFiltMaxGtAafHomRef() {
return threshFiltMaxGtAafHomRef;
}
public void setThreshFiltMaxGtAafHomRef(double threshFiltMaxGtAafHomRef) {
this.threshFiltMaxGtAafHomRef = threshFiltMaxGtAafHomRef;
}
public double getThreshFiltMaxAlleleFrequencyAd() {
return threshFiltMaxAlleleFrequencyAd;
}
public void setThreshFiltMaxAlleleFrequencyAD(double threshFiltMaxAlleleFrequencyAd) {
this.threshFiltMaxAlleleFrequencyAd = threshFiltMaxAlleleFrequencyAd;
}
public double getThreshFiltMaxAlleleFrequencyAr() {
return threshFiltMaxAlleleFrequencyAr;
}
public void setThreshFiltMaxAlleleFrequencyAR(double threshFiltMaxAlleleFrequencyAr) {
this.threshFiltMaxAlleleFrequencyAr = threshFiltMaxAlleleFrequencyAr;
}
public boolean isOffTargetFilterEnabled() {
return offTargetFilterEnabled;
}
public void setOffTargetFilterEnabled(boolean offTargetFilterEnabled) {
this.offTargetFilterEnabled = offTargetFilterEnabled;
}
public boolean isOffTargetFilterUtrIsOffTarget() {
return offTargetFilterUtrIsOffTarget;
}
public void setOffTargetFilterUtrIsOffTarget(boolean offTargetFilterUtrIsOffTarget) {
this.offTargetFilterUtrIsOffTarget = offTargetFilterUtrIsOffTarget;
}
public boolean isOffTargetFilterIntronicSpliceIsOffTarget() {
return offTargetFilterIntronicSpliceIsOffTarget;
}
public void setOffTargetFilterIntronicSpliceIsOffTarget(
boolean offTargetFilterIntronicSpliceIsOffTarget) {
this.offTargetFilterIntronicSpliceIsOffTarget = offTargetFilterIntronicSpliceIsOffTarget;
}
public void setThreshFiltMaxAlleleFrequencyAd(double threshFiltMaxAlleleFrequencyAd) {
this.threshFiltMaxAlleleFrequencyAd = threshFiltMaxAlleleFrequencyAd;
}
public void setThreshFiltMaxAlleleFrequencyAr(double threshFiltMaxAlleleFrequencyAr) {
this.threshFiltMaxAlleleFrequencyAr = threshFiltMaxAlleleFrequencyAr;
}
public boolean isInheritanceAnnoUseFilters() {
return inheritanceAnnoUseFilters;
}
public void setInheritanceAnnoUseFilters(boolean inheritanceAnnoUseFilters) {
this.inheritanceAnnoUseFilters = inheritanceAnnoUseFilters;
}
public boolean isUseAdvancedPedigreeFilters() {
return useAdvancedPedigreeFilters;
}
public void setUseAdvancedPedigreeFilters(boolean useAdvancedPedigreeFilters) {
this.useAdvancedPedigreeFilters = useAdvancedPedigreeFilters;
}
public List getBedAnnotationOptions() {
return bedAnnotationOptions;
}
public void setBedAnnotationOptions(List bedAnnotationOptions) {
this.bedAnnotationOptions = bedAnnotationOptions;
}
public Integer getThreshDeNovoParentAd2() {
return threshDeNovoParentAd2;
}
public void setThreshDeNovoParentAd2(Integer threshDeNovoParentAd2) {
this.threshDeNovoParentAd2 = threshDeNovoParentAd2;
}
public String getPrefixDbNsfp() {
return prefixDbNsfp;
}
public void setPrefixDbNsfp(String prefixDbNsfp) {
this.prefixDbNsfp = prefixDbNsfp;
}
public String getPathDbNsfp() {
return pathDbNsfp;
}
public void setPathDbNsfp(String pathDbNsfp) {
this.pathDbNsfp = pathDbNsfp;
}
public List getColumnsDbNsfp() {
return columnsDbNsfp;
}
public void setColumnsDbNsfp(List columnsDbNsfp) {
this.columnsDbNsfp = columnsDbNsfp;
}
public List getTsvAnnotationOptions() {
return tsvAnnotationOptions;
}
public void setTsvAnnotationOptions(List tsvAnnotationOptions) {
this.tsvAnnotationOptions = tsvAnnotationOptions;
}
public int getDbNsfpColContig() {
return dbNsfpColContig;
}
public void setDbNsfpColContig(int dbNsfpColContig) {
this.dbNsfpColContig = dbNsfpColContig;
}
public int getDbNsfpColPosition() {
return dbNsfpColPosition;
}
public void setDbNsfpColPosition(int dbNsfpColPosition) {
this.dbNsfpColPosition = dbNsfpColPosition;
}
public List getVcfAnnotationOptions() {
return vcfAnnotationOptions;
}
public void setVcfAnnotationOptions(List vcfAnnotationOptions) {
this.vcfAnnotationOptions = vcfAnnotationOptions;
}
public boolean isUseParentGtIsFiltered() {
return useParentGtIsFiltered;
}
public void setUseParentGtIsFiltered(boolean useParentGtIsFiltered) {
this.useParentGtIsFiltered = useParentGtIsFiltered;
}
@Override
public String toString() {
return "JannovarAnnotateVCFOptions [escapeAnnField=" + escapeAnnField + ", pathInputVCF="
+ pathInputVCF + ", interval=" + interval + ", pathOutputVCF=" + pathOutputVCF
+ ", pathVCFDBSNP=" + pathVCFDBSNP + ", prefixDBSNP=" + prefixDBSNP
+ ", pathFASTARef=" + pathFASTARef + ", pathVCFExac=" + pathVCFExac
+ ", prefixExac=" + prefixExac + ", pathVCFGnomadExomes=" + pathVCFGnomadExomes
+ ", prefixGnomadExomes=" + prefixGnomadExomes + ", pathVCFGnomadGenomes="
+ pathVCFGnomadGenomes + ", prefixGnomadGenomes=" + prefixGnomadGenomes
+ ", pathVCFUK10K=" + pathVCFUK10K + ", prefixUK10K=" + prefixUK10K
+ ", pathClinVar=" + pathClinVar + ", prefixClinVar=" + prefixClinVar
+ ", pathCosmic=" + pathCosmic + ", prefixCosmic=" + prefixCosmic + ", pathPedFile="
+ pathPedFile + ", annotateAsSingletonPedigree=" + annotateAsSingletonPedigree
+ ", useThresholdFilters=" + useThresholdFilters + ", useAdvancedPedigreeFilters="
+ useAdvancedPedigreeFilters + ", threshFiltMinGtCovHet=" + threshFiltMinGtCovHet
+ ", threshFiltMinGtCovHomAlt=" + threshFiltMinGtCovHomAlt + ", threshFiltMaxCov="
+ threshFiltMaxCov + ", threshFiltMinGtGq=" + threshFiltMinGtGq
+ ", threshFiltMinGtAafHet=" + threshFiltMinGtAafHet + ", threshFiltMaxGtAafHet="
+ threshFiltMaxGtAafHet + ", threshFiltMinGtAafHomAlt=" + threshFiltMinGtAafHomAlt
+ ", threshFiltMaxGtAafHomRef=" + threshFiltMaxGtAafHomRef
+ ", threshFiltMaxAlleleFrequencyAd=" + threshFiltMaxAlleleFrequencyAd
+ ", threshFiltMaxAlleleFrequencyAr=" + threshFiltMaxAlleleFrequencyAr
+ ", offTargetFilterEnabled=" + offTargetFilterEnabled
+ ", offTargetFilterUtrIsOffTarget=" + offTargetFilterUtrIsOffTarget
+ ", offTargetFilterIntronicSpliceIsOffTarget="
+ offTargetFilterIntronicSpliceIsOffTarget + ", inheritanceAnnoUseFilters="
+ inheritanceAnnoUseFilters + ", useParentGtIsFiltered=" + useParentGtIsFiltered
+ ", threshDeNovoParentAd2=" + threshDeNovoParentAd2 + ", bedAnnotationOptions="
+ bedAnnotationOptions + ", dbNsfpColContig=" + dbNsfpColContig
+ ", dbNsfpColPosition=" + dbNsfpColPosition + ", prefixDbNsfp=" + prefixDbNsfp
+ ", pathDbNsfp=" + pathDbNsfp + ", columnsDbNsfp=" + columnsDbNsfp
+ ", tsvAnnotationOptions=" + tsvAnnotationOptions + ", vcfAnnotationOptions="
+ vcfAnnotationOptions + "]";
}
/**
* Configuration for annotation with BED file.
*/
public static class BedAnnotationOptions {
/**
* Construct new BED annotation from command line option value.
*
*
* The value must have the format: pathToBed:infoField:description[:colNo]
*
*
* @param strValue String to parse from
* @return Constructed {@link BedAnnotationOptions} from the given string value.
*/
public static BedAnnotationOptions parseFrom(String strValue) {
String tokens[] = strValue.split(":", 4);
if (tokens.length < 3) {
throw new RuntimeException("Could not parse BED annotation from " + strValue);
} else if (tokens.length == 3) {
return new BedAnnotationOptions(tokens[0], tokens[1], tokens[2]);
} else {
return new BedAnnotationOptions(tokens[0], tokens[1], tokens[2],
Integer.parseInt(tokens[3]));
}
}
/** Path to BED file */
private final String pathBed;
/** Label to use for INFO field. */
private final String infoField;
/** Description to use for INFO field. */
private final String description;
/** 0-based column to write into VCF file, if any, -1 for none */
private final int colNo;
public BedAnnotationOptions(String pathBed, String infoField, String description) {
this(pathBed, infoField, description, -1);
}
public BedAnnotationOptions(String pathBed, String infoField, String description,
int colNo) {
this.pathBed = pathBed;
this.infoField = infoField;
this.description = description;
this.colNo = colNo;
}
public String getPathBed() {
return pathBed;
}
public int getColNo() {
return colNo;
}
public String getInfoField() {
return infoField;
}
public String getDescription() {
return description;
}
@Override
public String toString() {
return "BedAnnotationOptions [pathBed=" + pathBed + ", colNo=" + colNo + ", infoField="
+ infoField + ", description=" + description + "]";
}
}
}