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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<div class="contentContainer"><a href="#I:A">A</a> <a href="#I:B">B</a> <a href="#I:C">C</a> <a href="#I:D">D</a> <a href="#I:E">E</a> <a href="#I:F">F</a> <a href="#I:G">G</a> <a href="#I:H">H</a> <a href="#I:I">I</a> <a href="#I:L">L</a> <a href="#I:M">M</a> <a href="#I:N">N</a> <a href="#I:O">O</a> <a href="#I:P">P</a> <a href="#I:Q">Q</a> <a href="#I:R">R</a> <a href="#I:S">S</a> <a href="#I:T">T</a> <a href="#I:U">U</a> <a href="#I:V">V</a> <a href="#I:W">W</a> <a href="#I:X">X</a> <a href="#I:Z">Z</a> <a name="I:A">
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<h2 class="title">A</h2>
<dl>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/SimpleSemaphore.html#acquire--">acquire()</a></span> - Method in class no.uib.triogen.utils.<a href="no/uib/triogen/utils/SimpleSemaphore.html" title="class in no.uib.triogen.utils">SimpleSemaphore</a></dt>
<dd>
<div class="block">Acquires.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/metal/BoltToMetal.html#acThreshold">acThreshold</a></span> - Static variable in class no.uib.triogen.scripts_marc.metal.<a href="no/uib/triogen/scripts_marc/metal/BoltToMetal.html" title="class in no.uib.triogen.scripts_marc.metal">BoltToMetal</a></dt>
<dd>
<div class="block">Minor allele count should be strictly higher than this value.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/trio_genotypes/VariantIndex.html#add-java.lang.String-java.lang.String-">add(String, String)</a></span> - Method in class no.uib.triogen.model.trio_genotypes.<a href="no/uib/triogen/model/trio_genotypes/VariantIndex.html" title="class in no.uib.triogen.model.trio_genotypes">VariantIndex</a></dt>
<dd>
<div class="block">Adds a variant to the mapping and returns its index.</div>
</dd>
<dt><a href="no/uib/triogen/scripts_marc/metal/AddRsidToMetal.html" title="class in no.uib.triogen.scripts_marc.metal"><span class="typeNameLink">AddRsidToMetal</span></a> - Class in <a href="no/uib/triogen/scripts_marc/metal/package-summary.html">no.uib.triogen.scripts_marc.metal</a></dt>
<dd>
<div class="block">Attaches an rsid to metal results.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/metal/AddRsidToMetal.html#AddRsidToMetal--">AddRsidToMetal()</a></span> - Constructor for class no.uib.triogen.scripts_marc.metal.<a href="no/uib/triogen/scripts_marc/metal/AddRsidToMetal.html" title="class in no.uib.triogen.scripts_marc.metal">AddRsidToMetal</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/writer/BgenWriter.html#addVariant-no.uib.triogen.model.genome.VariantInformation-java.util.ArrayList-">addVariant(VariantInformation, ArrayList<String[]>)</a></span> - Method in class no.uib.triogen.io.genotypes.bgen.writer.<a href="no/uib/triogen/io/genotypes/bgen/writer/BgenWriter.html" title="class in no.uib.triogen.io.genotypes.bgen.writer">BgenWriter</a></dt>
<dd>
<div class="block">Adds a variant to the file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/ld/LdMatrixWriter.html#addVariant-int-java.util.ArrayList-io.airlift.compress.zstd.ZstdCompressor-">addVariant(int, ArrayList<R2>, ZstdCompressor)</a></span> - Method in class no.uib.triogen.io.ld.<a href="no/uib/triogen/io/ld/LdMatrixWriter.html" title="class in no.uib.triogen.io.ld">LdMatrixWriter</a></dt>
<dd>
<div class="block">Writes a variant to the file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/covariates/CovariatesHandler.html#adjustedIndexMap">adjustedIndexMap</a></span> - Variable in class no.uib.triogen.model.covariates.<a href="no/uib/triogen/model/covariates/CovariatesHandler.html" title="class in no.uib.triogen.model.covariates">CovariatesHandler</a></dt>
<dd>
<div class="block">The index of the children in the adjusted pheno values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/phenotypes/PhenotypesHandler.html#adjustForCovariates-java.lang.String:A-no.uib.triogen.model.covariates.CovariatesHandler-">adjustForCovariates(String[], CovariatesHandler)</a></span> - Method in class no.uib.triogen.model.phenotypes.<a href="no/uib/triogen/model/phenotypes/PhenotypesHandler.html" title="class in no.uib.triogen.model.phenotypes">PhenotypesHandler</a></dt>
<dd>
<div class="block">Projects phenotypes for the given pheno names using the covariates
handler.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html#afColumn">afColumn</a></span> - Variable in class no.uib.triogen.cmd.prs_prune.<a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html" title="class in no.uib.triogen.cmd.prs_prune">PrsPruneOptionsBean</a></dt>
<dd>
<div class="block">Column containing the allele frequency.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html#afColumn">afColumn</a></span> - Variable in class no.uib.triogen.cmd.prs_score.<a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html" title="class in no.uib.triogen.cmd.prs_score">PrsScoreOptionsBean</a></dt>
<dd>
<div class="block">Column containing the allele frequency.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html#afColumn">afColumn</a></span> - Variable in class no.uib.triogen.cmd.prs_threshold.<a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html" title="class in no.uib.triogen.cmd.prs_threshold">PrsThresholdOptionsBean</a></dt>
<dd>
<div class="block">Column containing the allele frequency.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html#afThreshold">afThreshold</a></span> - Variable in class no.uib.triogen.cmd.prs_prune.<a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html" title="class in no.uib.triogen.cmd.prs_prune">PrsPruneOptionsBean</a></dt>
<dd>
<div class="block">The allele frequency threshold.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html#afThreshold">afThreshold</a></span> - Variable in class no.uib.triogen.cmd.prs_score.<a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html" title="class in no.uib.triogen.cmd.prs_score">PrsScoreOptionsBean</a></dt>
<dd>
<div class="block">The allele frequency threshold.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html#afThreshold">afThreshold</a></span> - Variable in class no.uib.triogen.cmd.prs_threshold.<a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html" title="class in no.uib.triogen.cmd.prs_threshold">PrsThresholdOptionsBean</a></dt>
<dd>
<div class="block">The allele frequency threshold.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/ld/R2.html#alleleA">alleleA</a></span> - Variable in class no.uib.triogen.model.ld.<a href="no/uib/triogen/model/ld/R2.html" title="class in no.uib.triogen.model.ld">R2</a></dt>
<dd>
<div class="block">The correlated allele for variant A.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/ld/R2.html#alleleB">alleleB</a></span> - Variable in class no.uib.triogen.model.ld.<a href="no/uib/triogen/model/ld/R2.html" title="class in no.uib.triogen.model.ld">R2</a></dt>
<dd>
<div class="block">The correlated allele for variant B.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html#alleleFrequencyThreshold">alleleFrequencyThreshold</a></span> - Variable in class no.uib.triogen.cmd.association.<a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html" title="class in no.uib.triogen.cmd.association">LinearModelOptionsBean</a></dt>
<dd>
<div class="block">The allele frequency threshold.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptionsBean.html#alleleFrequencyThreshold">alleleFrequencyThreshold</a></span> - Variable in class no.uib.triogen.cmd.ld_matrix.<a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptionsBean.html" title="class in no.uib.triogen.cmd.ld_matrix">LdMatrixOptionsBean</a></dt>
<dd>
<div class="block">The allele frequency threshold.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptionsBean.html#alleleFrequencyThreshold">alleleFrequencyThreshold</a></span> - Variable in class no.uib.triogen.cmd.mendelian_check.<a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptionsBean.html" title="class in no.uib.triogen.cmd.mendelian_check">MendelianCheckOptionsBean</a></dt>
<dd>
<div class="block">The allele frequency threshold.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/annotation/ProxyCoordinates.html#alleleMapping">alleleMapping</a></span> - Variable in class no.uib.triogen.model.annotation.<a href="no/uib/triogen/model/annotation/ProxyCoordinates.html" title="class in no.uib.triogen.model.annotation">ProxyCoordinates</a></dt>
<dd>
<div class="block">The allele mapping.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/genome/VariantInformation.html#alleles">alleles</a></span> - Variable in class no.uib.triogen.model.genome.<a href="no/uib/triogen/model/genome/VariantInformation.html" title="class in no.uib.triogen.model.genome">VariantInformation</a></dt>
<dd>
<div class="block">The alleles.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/indexed/IndexedGzWriter.html#append-java.lang.String-">append(String)</a></span> - Method in class no.uib.triogen.io.flat.indexed.<a href="no/uib/triogen/io/flat/indexed/IndexedGzWriter.html" title="class in no.uib.triogen.io.flat.indexed">IndexedGzWriter</a></dt>
<dd>
<div class="block">Appends a String to the file and returns the coordinates of the file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/RegressionResult.html#appendResults-java.lang.StringBuilder-">appendResults(StringBuilder)</a></span> - Method in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/RegressionResult.html" title="class in no.uib.triogen.processing.linear_model">RegressionResult</a></dt>
<dd>
<div class="block">Appends the regression results to the given string builder.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/TempByteArray.html#array">array</a></span> - Variable in class no.uib.triogen.utils.<a href="no/uib/triogen/utils/TempByteArray.html" title="class in no.uib.triogen.utils">TempByteArray</a></dt>
<dd>
<div class="block">The byte array.</div>
</dd>
</dl>
<a name="I:B">
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<h2 class="title">B</h2>
<dl>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/cadd/CaddToSql.html#BATCH_SIZE">BATCH_SIZE</a></span> - Static variable in class no.uib.triogen.scripts_marc.cadd.<a href="no/uib/triogen/scripts_marc/cadd/CaddToSql.html" title="class in no.uib.triogen.scripts_marc.cadd">CaddToSql</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/RegressionResult.html#beta">beta</a></span> - Variable in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/RegressionResult.html" title="class in no.uib.triogen.processing.linear_model">RegressionResult</a></dt>
<dd>
<div class="block">Estimates for the slopes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/prs/PrsThresholder.html#BETA_QUANTILES">BETA_QUANTILES</a></span> - Static variable in class no.uib.triogen.processing.prs.<a href="no/uib/triogen/processing/prs/PrsThresholder.html" title="class in no.uib.triogen.processing.prs">PrsThresholder</a></dt>
<dd>
<div class="block">The beta quantiles to try.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/trio_genotypes/Model.html#betaNames">betaNames</a></span> - Variable in enum no.uib.triogen.model.trio_genotypes.<a href="no/uib/triogen/model/trio_genotypes/Model.html" title="enum in no.uib.triogen.model.trio_genotypes">Model</a></dt>
<dd>
<div class="block">The names of the betas to estimate.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html#betaPattern">betaPattern</a></span> - Variable in class no.uib.triogen.cmd.prs_prune.<a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html" title="class in no.uib.triogen.cmd.prs_prune">PrsPruneOptionsBean</a></dt>
<dd>
<div class="block">Pattern for the effect size column.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html#betaPattern">betaPattern</a></span> - Variable in class no.uib.triogen.cmd.prs_score.<a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html" title="class in no.uib.triogen.cmd.prs_score">PrsScoreOptionsBean</a></dt>
<dd>
<div class="block">Pattern for the effect size column.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html#betaPattern">betaPattern</a></span> - Variable in class no.uib.triogen.cmd.prs_threshold.<a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html" title="class in no.uib.triogen.cmd.prs_threshold">PrsThresholdOptionsBean</a></dt>
<dd>
<div class="block">Pattern for the effect size column.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html#betaQuantile">betaQuantile</a></span> - Variable in class no.uib.triogen.cmd.prs_score.<a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html" title="class in no.uib.triogen.cmd.prs_score">PrsScoreOptionsBean</a></dt>
<dd>
<div class="block">The quantile to use for beta estimation.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html#betaQuantile">betaQuantile</a></span> - Variable in class no.uib.triogen.cmd.prs_threshold.<a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html" title="class in no.uib.triogen.cmd.prs_threshold">PrsThresholdOptionsBean</a></dt>
<dd>
<div class="block">The quantile to use for beta estimation.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/RegressionResult.html#betaResiduals">betaResiduals</a></span> - Variable in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/RegressionResult.html" title="class in no.uib.triogen.processing.linear_model">RegressionResult</a></dt>
<dd>
<div class="block">Residuals.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/RegressionResult.html#betaSignificance">betaSignificance</a></span> - Variable in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/RegressionResult.html" title="class in no.uib.triogen.processing.linear_model">RegressionResult</a></dt>
<dd>
<div class="block">Estimates for the significance of the slopes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/RegressionResult.html#betaStandardError">betaStandardError</a></span> - Variable in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/RegressionResult.html" title="class in no.uib.triogen.processing.linear_model">RegressionResult</a></dt>
<dd>
<div class="block">Standard error of the slope estimate.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/vcf_to_bgen/VcfToBgenOptionsBean.html#bgenFile">bgenFile</a></span> - Variable in class no.uib.triogen.cmd.vcf_to_bgen.<a href="no/uib/triogen/cmd/vcf_to_bgen/VcfToBgenOptionsBean.html" title="class in no.uib.triogen.cmd.vcf_to_bgen">VcfToBgenOptionsBean</a></dt>
<dd>
<div class="block">The bgen file.</div>
</dd>
<dt><a href="no/uib/triogen/io/genotypes/bgen/reader/BgenFileReader.html" title="class in no.uib.triogen.io.genotypes.bgen.reader"><span class="typeNameLink">BgenFileReader</span></a> - Class in <a href="no/uib/triogen/io/genotypes/bgen/reader/package-summary.html">no.uib.triogen.io.genotypes.bgen.reader</a></dt>
<dd>
<div class="block">Reader for a Bgen file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/reader/BgenFileReader.html#BgenFileReader-java.io.File-no.uib.triogen.io.genotypes.bgen.index.BgenIndex-java.util.HashMap-int-int-">BgenFileReader(File, BgenIndex, HashMap<Integer, char[]>, int, int)</a></span> - Constructor for class no.uib.triogen.io.genotypes.bgen.reader.<a href="no/uib/triogen/io/genotypes/bgen/reader/BgenFileReader.html" title="class in no.uib.triogen.io.genotypes.bgen.reader">BgenFileReader</a></dt>
<dd>
<div class="block">Constructor.</div>
</dd>
<dt><a href="no/uib/triogen/io/genotypes/bgen/index/BgenIndex.html" title="class in no.uib.triogen.io.genotypes.bgen.index"><span class="typeNameLink">BgenIndex</span></a> - Class in <a href="no/uib/triogen/io/genotypes/bgen/index/package-summary.html">no.uib.triogen.io.genotypes.bgen.index</a></dt>
<dd>
<div class="block">Index for a bgen file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/index/BgenIndex.html#BgenIndex-java.lang.String:A-no.uib.triogen.model.genome.VariantInformation:A-long:A-long:A-java.lang.String:A-int-">BgenIndex(String[], VariantInformation[], long[], long[], String[], int)</a></span> - Constructor for class no.uib.triogen.io.genotypes.bgen.index.<a href="no/uib/triogen/io/genotypes/bgen/index/BgenIndex.html" title="class in no.uib.triogen.io.genotypes.bgen.index">BgenIndex</a></dt>
<dd>
<div class="block">Constructor.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html#bgenIndexFolder">bgenIndexFolder</a></span> - Variable in class no.uib.triogen.cmd.prs_score.<a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html" title="class in no.uib.triogen.cmd.prs_score">PrsScoreOptionsBean</a></dt>
<dd>
<div class="block">The folder where to store the bgen index files.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html#bgenIndexFolder">bgenIndexFolder</a></span> - Variable in class no.uib.triogen.cmd.prs_threshold.<a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html" title="class in no.uib.triogen.cmd.prs_threshold">PrsThresholdOptionsBean</a></dt>
<dd>
<div class="block">The folder where to store the bgen index files.</div>
</dd>
<dt><a href="no/uib/triogen/io/genotypes/bgen/BgenUtils.html" title="class in no.uib.triogen.io.genotypes.bgen"><span class="typeNameLink">BgenUtils</span></a> - Class in <a href="no/uib/triogen/io/genotypes/bgen/package-summary.html">no.uib.triogen.io.genotypes.bgen</a></dt>
<dd>
<div class="block">Utils for the reading of bgen files.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/BgenUtils.html#BgenUtils--">BgenUtils()</a></span> - Constructor for class no.uib.triogen.io.genotypes.bgen.<a href="no/uib/triogen/io/genotypes/bgen/BgenUtils.html" title="class in no.uib.triogen.io.genotypes.bgen">BgenUtils</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/io/genotypes/bgen/variant_data/BgenVariantTrioData.html" title="class in no.uib.triogen.io.genotypes.bgen.variant_data"><span class="typeNameLink">BgenVariantTrioData</span></a> - Class in <a href="no/uib/triogen/io/genotypes/bgen/variant_data/package-summary.html">no.uib.triogen.io.genotypes.bgen.variant_data</a></dt>
<dd>
<div class="block">Trio-based genotypes provider based on a bgen file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/variant_data/BgenVariantTrioData.html#BgenVariantTrioData-java.lang.String:A-no.uib.triogen.model.genome.VariantInformation-java.nio.MappedByteBuffer-int-int-java.util.HashMap-int-int-">BgenVariantTrioData(String[], VariantInformation, MappedByteBuffer, int, int, HashMap<Integer, char[]>, int, int)</a></span> - Constructor for class no.uib.triogen.io.genotypes.bgen.variant_data.<a href="no/uib/triogen/io/genotypes/bgen/variant_data/BgenVariantTrioData.html" title="class in no.uib.triogen.io.genotypes.bgen.variant_data">BgenVariantTrioData</a></dt>
<dd>
<div class="block">Constructor.</div>
</dd>
<dt><a href="no/uib/triogen/io/genotypes/bgen/writer/BgenWriter.html" title="class in no.uib.triogen.io.genotypes.bgen.writer"><span class="typeNameLink">BgenWriter</span></a> - Class in <a href="no/uib/triogen/io/genotypes/bgen/writer/package-summary.html">no.uib.triogen.io.genotypes.bgen.writer</a></dt>
<dd>
<div class="block">Writer for a bgen file with phased haplotypes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/writer/BgenWriter.html#BgenWriter-java.io.File-java.io.File-">BgenWriter(File, File)</a></span> - Constructor for class no.uib.triogen.io.genotypes.bgen.writer.<a href="no/uib/triogen/io/genotypes/bgen/writer/BgenWriter.html" title="class in no.uib.triogen.io.genotypes.bgen.writer">BgenWriter</a></dt>
<dd>
<div class="block">Constructor.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/Utils.html#bin-double:A-int-">bin(double[], int)</a></span> - Static method in class no.uib.triogen.utils.<a href="no/uib/triogen/utils/Utils.html" title="class in no.uib.triogen.utils">Utils</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/annotation/ensembl/GeneCoordinates.html#biotype">biotype</a></span> - Variable in class no.uib.triogen.model.annotation.ensembl.<a href="no/uib/triogen/model/annotation/ensembl/GeneCoordinates.html" title="class in no.uib.triogen.model.annotation.ensembl">GeneCoordinates</a></dt>
<dd>
<div class="block">The biotype.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/ld/P0Cache.html#block-int-int-">block(int, int)</a></span> - Method in class no.uib.triogen.processing.ld.<a href="no/uib/triogen/processing/ld/P0Cache.html" title="class in no.uib.triogen.processing.ld">P0Cache</a></dt>
<dd>
<div class="block">Releases the given position for the given thread.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/ld/LdMatrixReader.html#BLOCK_SIZE">BLOCK_SIZE</a></span> - Static variable in class no.uib.triogen.io.ld.<a href="no/uib/triogen/io/ld/LdMatrixReader.html" title="class in no.uib.triogen.io.ld">LdMatrixReader</a></dt>
<dd>
<div class="block">The block size to use for the memory mapped file.</div>
</dd>
<dt><a href="no/uib/triogen/scripts_marc/bolt/BoltCleanUp.html" title="class in no.uib.triogen.scripts_marc.bolt"><span class="typeNameLink">BoltCleanUp</span></a> - Class in <a href="no/uib/triogen/scripts_marc/bolt/package-summary.html">no.uib.triogen.scripts_marc.bolt</a></dt>
<dd>
<div class="block">This script Cleans the organization of BOLT-LMM files on MoBa.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/bolt/BoltCleanUp.html#BoltCleanUp--">BoltCleanUp()</a></span> - Constructor for class no.uib.triogen.scripts_marc.bolt.<a href="no/uib/triogen/scripts_marc/bolt/BoltCleanUp.html" title="class in no.uib.triogen.scripts_marc.bolt">BoltCleanUp</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/mobarun/BoltCleanUp.html" title="class in no.uib.triogen.scripts_marc.mobarun"><span class="typeNameLink">BoltCleanUp</span></a> - Class in <a href="no/uib/triogen/scripts_marc/mobarun/package-summary.html">no.uib.triogen.scripts_marc.mobarun</a></dt>
<dd>
<div class="block">This script Cleans the organization of BOLT-LMM files on MoBa.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/mobarun/BoltCleanUp.html#BoltCleanUp--">BoltCleanUp()</a></span> - Constructor for class no.uib.triogen.scripts_marc.mobarun.<a href="no/uib/triogen/scripts_marc/mobarun/BoltCleanUp.html" title="class in no.uib.triogen.scripts_marc.mobarun">BoltCleanUp</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/metal/BoltToMetal.html" title="class in no.uib.triogen.scripts_marc.metal"><span class="typeNameLink">BoltToMetal</span></a> - Class in <a href="no/uib/triogen/scripts_marc/metal/package-summary.html">no.uib.triogen.scripts_marc.metal</a></dt>
<dd>
<div class="block">Converts BOLT-LMM results to metal</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/metal/BoltToMetal.html#BoltToMetal--">BoltToMetal()</a></span> - Constructor for class no.uib.triogen.scripts_marc.metal.<a href="no/uib/triogen/scripts_marc/metal/BoltToMetal.html" title="class in no.uib.triogen.scripts_marc.metal">BoltToMetal</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/mobarun/BoltToTargetFile.html" title="class in no.uib.triogen.scripts_marc.mobarun"><span class="typeNameLink">BoltToTargetFile</span></a> - Class in <a href="no/uib/triogen/scripts_marc/mobarun/package-summary.html">no.uib.triogen.scripts_marc.mobarun</a></dt>
<dd>
<div class="block">This script generates a target file from a Bolt results file</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/mobarun/BoltToTargetFile.html#BoltToTargetFile--">BoltToTargetFile()</a></span> - Constructor for class no.uib.triogen.scripts_marc.mobarun.<a href="no/uib/triogen/scripts_marc/mobarun/BoltToTargetFile.html" title="class in no.uib.triogen.scripts_marc.mobarun">BoltToTargetFile</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptionsBean.html#buildNumber">buildNumber</a></span> - Variable in class no.uib.triogen.cmd.ld_pruning.<a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptionsBean.html" title="class in no.uib.triogen.cmd.ld_pruning">LdPruningOptionsBean</a></dt>
<dd>
<div class="block">The build number.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/locus/LocusZoomOptionsBean.html#buildNumber">buildNumber</a></span> - Variable in class no.uib.triogen.cmd.locus.<a href="no/uib/triogen/cmd/locus/LocusZoomOptionsBean.html" title="class in no.uib.triogen.cmd.locus">LocusZoomOptionsBean</a></dt>
<dd>
<div class="block">The number of the build, e.g.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_file/VariantFileOptionsBean.html#buildNumber">buildNumber</a></span> - Variable in class no.uib.triogen.cmd.variant_file.<a href="no/uib/triogen/cmd/variant_file/VariantFileOptionsBean.html" title="class in no.uib.triogen.cmd.variant_file">VariantFileOptionsBean</a></dt>
<dd>
<div class="block">The build number.</div>
</dd>
</dl>
<a name="I:C">
<!-- -->
</a>
<h2 class="title">C</h2>
<dl>
<dt><a href="no/uib/triogen/scripts_marc/cadd/CaddToIndexedGz.html" title="class in no.uib.triogen.scripts_marc.cadd"><span class="typeNameLink">CaddToIndexedGz</span></a> - Class in <a href="no/uib/triogen/scripts_marc/cadd/package-summary.html">no.uib.triogen.scripts_marc.cadd</a></dt>
<dd>
<div class="block">Puts the cadd database in an line-indexed gz file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/cadd/CaddToIndexedGz.html#CaddToIndexedGz--">CaddToIndexedGz()</a></span> - Constructor for class no.uib.triogen.scripts_marc.cadd.<a href="no/uib/triogen/scripts_marc/cadd/CaddToIndexedGz.html" title="class in no.uib.triogen.scripts_marc.cadd">CaddToIndexedGz</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/cadd/CaddToRaf.html" title="class in no.uib.triogen.scripts_marc.cadd"><span class="typeNameLink">CaddToRaf</span></a> - Class in <a href="no/uib/triogen/scripts_marc/cadd/package-summary.html">no.uib.triogen.scripts_marc.cadd</a></dt>
<dd>
<div class="block">Puts the cadd database in a raf file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/cadd/CaddToRaf.html#CaddToRaf--">CaddToRaf()</a></span> - Constructor for class no.uib.triogen.scripts_marc.cadd.<a href="no/uib/triogen/scripts_marc/cadd/CaddToRaf.html" title="class in no.uib.triogen.scripts_marc.cadd">CaddToRaf</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/cadd/CaddToSql.html" title="class in no.uib.triogen.scripts_marc.cadd"><span class="typeNameLink">CaddToSql</span></a> - Class in <a href="no/uib/triogen/scripts_marc/cadd/package-summary.html">no.uib.triogen.scripts_marc.cadd</a></dt>
<dd>
<div class="block">Puts the cadd database in an SQLite database.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/cadd/CaddToSql.html#CaddToSql--">CaddToSql()</a></span> - Constructor for class no.uib.triogen.scripts_marc.cadd.<a href="no/uib/triogen/scripts_marc/cadd/CaddToSql.html" title="class in no.uib.triogen.scripts_marc.cadd">CaddToSql</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/Utils.html#centerAndScale-double:A-">centerAndScale(double[])</a></span> - Static method in class no.uib.triogen.utils.<a href="no/uib/triogen/utils/Utils.html" title="class in no.uib.triogen.utils">Utils</a></dt>
<dd>
<div class="block">Centers and scales the values in x using the mean and standard deviation.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/BgenUtils.html#checkMagicNumber-byte:A-">checkMagicNumber(byte[])</a></span> - Static method in class no.uib.triogen.io.genotypes.bgen.<a href="no/uib/triogen/io/genotypes/bgen/BgenUtils.html" title="class in no.uib.triogen.io.genotypes.bgen">BgenUtils</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/phenotypes/PhenotypesHandler.html#childIdColumn">childIdColumn</a></span> - Static variable in class no.uib.triogen.model.phenotypes.<a href="no/uib/triogen/model/phenotypes/PhenotypesHandler.html" title="class in no.uib.triogen.model.phenotypes">PhenotypesHandler</a></dt>
<dd>
<div class="block">Name of the column containing the child ids.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/family/ChildToParentMap.html#children">children</a></span> - Variable in class no.uib.triogen.model.family.<a href="no/uib/triogen/model/family/ChildToParentMap.html" title="class in no.uib.triogen.model.family">ChildToParentMap</a></dt>
<dd>
<div class="block">Ordered array of children.</div>
</dd>
<dt><a href="no/uib/triogen/model/family/ChildToParentMap.html" title="class in no.uib.triogen.model.family"><span class="typeNameLink">ChildToParentMap</span></a> - Class in <a href="no/uib/triogen/model/family/package-summary.html">no.uib.triogen.model.family</a></dt>
<dd>
<div class="block">This class contains mapping between trios.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/family/ChildToParentMap.html#ChildToParentMap-java.lang.String:A-java.util.HashMap-java.util.HashMap-">ChildToParentMap(String[], HashMap<String, String>, HashMap<String, String>)</a></span> - Constructor for class no.uib.triogen.model.family.<a href="no/uib/triogen/model/family/ChildToParentMap.html" title="class in no.uib.triogen.model.family">ChildToParentMap</a></dt>
<dd>
<div class="block">Constructor.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html#chrColumn">chrColumn</a></span> - Variable in class no.uib.triogen.cmd.prs_prune.<a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html" title="class in no.uib.triogen.cmd.prs_prune">PrsPruneOptionsBean</a></dt>
<dd>
<div class="block">Name of the contig column in the training file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html#chromosome">chromosome</a></span> - Variable in class no.uib.triogen.cmd.association.<a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html" title="class in no.uib.triogen.cmd.association">LinearModelOptionsBean</a></dt>
<dd>
<div class="block">The chromosome name.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptionsBean.html#chromosome">chromosome</a></span> - Variable in class no.uib.triogen.cmd.ld_matrix.<a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptionsBean.html" title="class in no.uib.triogen.cmd.ld_matrix">LdMatrixOptionsBean</a></dt>
<dd>
<div class="block">The chromosome name.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptionsBean.html#chromosome">chromosome</a></span> - Variable in class no.uib.triogen.cmd.mendelian_check.<a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptionsBean.html" title="class in no.uib.triogen.cmd.mendelian_check">MendelianCheckOptionsBean</a></dt>
<dd>
<div class="block">The chromosome name.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/simple_score/SimpleScoreOptionsBean.html#chromosome">chromosome</a></span> - Variable in class no.uib.triogen.cmd.simple_score.<a href="no/uib/triogen/cmd/simple_score/SimpleScoreOptionsBean.html" title="class in no.uib.triogen.cmd.simple_score">SimpleScoreOptionsBean</a></dt>
<dd>
<div class="block">The chromosome name.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_data/VariantDataOptionsBean.html#chromosome">chromosome</a></span> - Variable in class no.uib.triogen.cmd.variant_data.<a href="no/uib/triogen/cmd/variant_data/VariantDataOptionsBean.html" title="class in no.uib.triogen.cmd.variant_data">VariantDataOptionsBean</a></dt>
<dd>
<div class="block">The chromosome name.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/trio_genotypes/VariantList.html#chromosome">chromosome</a></span> - Variable in class no.uib.triogen.model.trio_genotypes.<a href="no/uib/triogen/model/trio_genotypes/VariantList.html" title="class in no.uib.triogen.model.trio_genotypes">VariantList</a></dt>
<dd>
<div class="block">The name of the contig.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/Utils.html#CHROMOSOME_WILDCARD">CHROMOSOME_WILDCARD</a></span> - Static variable in class no.uib.triogen.utils.<a href="no/uib/triogen/utils/Utils.html" title="class in no.uib.triogen.utils">Utils</a></dt>
<dd>
<div class="block">Wildcard for the chromosome name in the genotypes file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/genome/ChromosomeUtils.html#chromosomeLength37">chromosomeLength37</a></span> - Static variable in class no.uib.triogen.model.genome.<a href="no/uib/triogen/model/genome/ChromosomeUtils.html" title="class in no.uib.triogen.model.genome">ChromosomeUtils</a></dt>
<dd>
<div class="block">Map of the chromosome length in BP in GRCh37.p13 (hg19) from Ensembl.</div>
</dd>
<dt><a href="no/uib/triogen/model/genome/ChromosomeUtils.html" title="class in no.uib.triogen.model.genome"><span class="typeNameLink">ChromosomeUtils</span></a> - Class in <a href="no/uib/triogen/model/genome/package-summary.html">no.uib.triogen.model.genome</a></dt>
<dd>
<div class="block">Convenience data and functions for chromosomes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/genome/ChromosomeUtils.html#ChromosomeUtils--">ChromosomeUtils()</a></span> - Constructor for class no.uib.triogen.model.genome.<a href="no/uib/triogen/model/genome/ChromosomeUtils.html" title="class in no.uib.triogen.model.genome">ChromosomeUtils</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/ld/P0Cache.html#cleanCache--">cleanCache()</a></span> - Method in class no.uib.triogen.processing.ld.<a href="no/uib/triogen/processing/ld/P0Cache.html" title="class in no.uib.triogen.processing.ld">P0Cache</a></dt>
<dd>
<div class="block">Clear information from the cache.</div>
</dd>
<dt><a href="no/uib/triogen/scripts_marc/metal/CleanMeta.html" title="class in no.uib.triogen.scripts_marc.metal"><span class="typeNameLink">CleanMeta</span></a> - Class in <a href="no/uib/triogen/scripts_marc/metal/package-summary.html">no.uib.triogen.scripts_marc.metal</a></dt>
<dd>
<div class="block">Convenience script cleaning the results of the pw meta.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/metal/CleanMeta.html#CleanMeta--">CleanMeta()</a></span> - Constructor for class no.uib.triogen.scripts_marc.metal.<a href="no/uib/triogen/scripts_marc/metal/CleanMeta.html" title="class in no.uib.triogen.scripts_marc.metal">CleanMeta</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/metal/CleanPwMeta.html" title="class in no.uib.triogen.scripts_marc.metal"><span class="typeNameLink">CleanPwMeta</span></a> - Class in <a href="no/uib/triogen/scripts_marc/metal/package-summary.html">no.uib.triogen.scripts_marc.metal</a></dt>
<dd>
<div class="block">Filters and arranges the results of the meta for Pw.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/metal/CleanPwMeta.html#CleanPwMeta--">CleanPwMeta()</a></span> - Constructor for class no.uib.triogen.scripts_marc.metal.<a href="no/uib/triogen/scripts_marc/metal/CleanPwMeta.html" title="class in no.uib.triogen.scripts_marc.metal">CleanPwMeta</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/utils/cli/CliOption.html" title="interface in no.uib.triogen.utils.cli"><span class="typeNameLink">CliOption</span></a> - Interface in <a href="no/uib/triogen/utils/cli/package-summary.html">no.uib.triogen.utils.cli</a></dt>
<dd>
<div class="block">Interface for a CLI option.</div>
</dd>
<dt><a href="no/uib/triogen/utils/cli/CliUtils.html" title="class in no.uib.triogen.utils.cli"><span class="typeNameLink">CliUtils</span></a> - Class in <a href="no/uib/triogen/utils/cli/package-summary.html">no.uib.triogen.utils.cli</a></dt>
<dd>
<div class="block">Convenience methods for command line handling.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/cli/CliUtils.html#CliUtils--">CliUtils()</a></span> - Constructor for class no.uib.triogen.utils.cli.<a href="no/uib/triogen/utils/cli/CliUtils.html" title="class in no.uib.triogen.utils.cli">CliUtils</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/indexed/IndexedGzReader.html#close--">close()</a></span> - Method in class no.uib.triogen.io.flat.indexed.<a href="no/uib/triogen/io/flat/indexed/IndexedGzReader.html" title="class in no.uib.triogen.io.flat.indexed">IndexedGzReader</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/indexed/IndexedGzWriter.html#close--">close()</a></span> - Method in class no.uib.triogen.io.flat.indexed.<a href="no/uib/triogen/io/flat/indexed/IndexedGzWriter.html" title="class in no.uib.triogen.io.flat.indexed">IndexedGzWriter</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/mapping/MemoryMappedFile.html#close--">close()</a></span> - Method in class no.uib.triogen.io.flat.mapping.<a href="no/uib/triogen/io/flat/mapping/MemoryMappedFile.html" title="class in no.uib.triogen.io.flat.mapping">MemoryMappedFile</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/mapping/MemoryMappedFile.MiniBuffer.html#close--">close()</a></span> - Method in class no.uib.triogen.io.flat.mapping.<a href="no/uib/triogen/io/flat/mapping/MemoryMappedFile.MiniBuffer.html" title="class in no.uib.triogen.io.flat.mapping">MemoryMappedFile.MiniBuffer</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/readers/SimpleGzReader.html#close--">close()</a></span> - Method in class no.uib.triogen.io.flat.readers.<a href="no/uib/triogen/io/flat/readers/SimpleGzReader.html" title="class in no.uib.triogen.io.flat.readers">SimpleGzReader</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/readers/SimpleTextReader.html#close--">close()</a></span> - Method in class no.uib.triogen.io.flat.readers.<a href="no/uib/triogen/io/flat/readers/SimpleTextReader.html" title="class in no.uib.triogen.io.flat.readers">SimpleTextReader</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/SimpleFileReader.html#close--">close()</a></span> - Method in interface no.uib.triogen.io.flat.<a href="no/uib/triogen/io/flat/SimpleFileReader.html" title="interface in no.uib.triogen.io.flat">SimpleFileReader</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/SimpleFileWriter.html#close--">close()</a></span> - Method in class no.uib.triogen.io.flat.<a href="no/uib/triogen/io/flat/SimpleFileWriter.html" title="class in no.uib.triogen.io.flat">SimpleFileWriter</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/reader/BgenFileReader.html#close--">close()</a></span> - Method in class no.uib.triogen.io.genotypes.bgen.reader.<a href="no/uib/triogen/io/genotypes/bgen/reader/BgenFileReader.html" title="class in no.uib.triogen.io.genotypes.bgen.reader">BgenFileReader</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/writer/BgenWriter.html#close--">close()</a></span> - Method in class no.uib.triogen.io.genotypes.bgen.writer.<a href="no/uib/triogen/io/genotypes/bgen/writer/BgenWriter.html" title="class in no.uib.triogen.io.genotypes.bgen.writer">BgenWriter</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/vcf/iterators/VcfIterator.html#close--">close()</a></span> - Method in class no.uib.triogen.io.genotypes.vcf.iterators.<a href="no/uib/triogen/io/genotypes/vcf/iterators/VcfIterator.html" title="class in no.uib.triogen.io.genotypes.vcf.iterators">VcfIterator</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/ld/LdMatrixReader.html#close--">close()</a></span> - Method in class no.uib.triogen.io.ld.<a href="no/uib/triogen/io/ld/LdMatrixReader.html" title="class in no.uib.triogen.io.ld">LdMatrixReader</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/ld/LdMatrixWriter.html#close--">close()</a></span> - Method in class no.uib.triogen.io.ld.<a href="no/uib/triogen/io/ld/LdMatrixWriter.html" title="class in no.uib.triogen.io.ld">LdMatrixWriter</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/log/SimpleCliLogger.html#close--">close()</a></span> - Method in class no.uib.triogen.log.<a href="no/uib/triogen/log/SimpleCliLogger.html" title="class in no.uib.triogen.log">SimpleCliLogger</a></dt>
<dd>
<div class="block">Closes the logger.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/IoUtils.html#closeBuffer-java.nio.MappedByteBuffer-">closeBuffer(MappedByteBuffer)</a></span> - Static method in class no.uib.triogen.io.<a href="no/uib/triogen/io/IoUtils.html" title="class in no.uib.triogen.io">IoUtils</a></dt>
<dd>
<div class="block">Attempts at closing a buffer to avoid memory issues.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/extract/ExtractOptionsBean.html#columns">columns</a></span> - Variable in class no.uib.triogen.cmd.extract.<a href="no/uib/triogen/cmd/extract/ExtractOptionsBean.html" title="class in no.uib.triogen.cmd.extract">ExtractOptionsBean</a></dt>
<dd>
<div class="block">The columns.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/indexed/IndexedGzCoordinates.html#compressedLength">compressedLength</a></span> - Variable in class no.uib.triogen.io.flat.indexed.<a href="no/uib/triogen/io/flat/indexed/IndexedGzCoordinates.html" title="class in no.uib.triogen.io.flat.indexed">IndexedGzCoordinates</a></dt>
<dd>
<div class="block">Length of the compressed byte array.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/index/BgenIndex.html#compressionType">compressionType</a></span> - Variable in class no.uib.triogen.io.genotypes.bgen.index.<a href="no/uib/triogen/io/genotypes/bgen/index/BgenIndex.html" title="class in no.uib.triogen.io.genotypes.bgen.index">BgenIndex</a></dt>
<dd>
<div class="block">The compression type according to the format specifications.</div>
</dd>
<dt><a href="no/uib/triogen/utils/CompressionUtils.html" title="class in no.uib.triogen.utils"><span class="typeNameLink">CompressionUtils</span></a> - Class in <a href="no/uib/triogen/utils/package-summary.html">no.uib.triogen.utils</a></dt>
<dd>
<div class="block">Functions needed for compression and decompression.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/CompressionUtils.html#CompressionUtils--">CompressionUtils()</a></span> - Constructor for class no.uib.triogen.utils.<a href="no/uib/triogen/utils/CompressionUtils.html" title="class in no.uib.triogen.utils">CompressionUtils</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/RegressionResult.html#computeBetaSignificance--">computeBetaSignificance()</a></span> - Method in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/RegressionResult.html" title="class in no.uib.triogen.processing.linear_model">RegressionResult</a></dt>
<dd>
<div class="block">Computes the significance the beta estimates.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/Utils.html#computeBetaSignificance-int-int-double-double-">computeBetaSignificance(int, int, double, double)</a></span> - Method in class no.uib.triogen.utils.<a href="no/uib/triogen/utils/Utils.html" title="class in no.uib.triogen.utils">Utils</a></dt>
<dd>
<div class="block">Computes the significance the beta estimates.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/Utils.html#computeBetaSignificance-double-double-">computeBetaSignificance(double, double)</a></span> - Static method in class no.uib.triogen.utils.<a href="no/uib/triogen/utils/Utils.html" title="class in no.uib.triogen.utils">Utils</a></dt>
<dd>
<div class="block">Computes the significance the beta estimates.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/RegressionResult.html#computeModelSignificance-double-">computeModelSignificance(double)</a></span> - Method in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/RegressionResult.html" title="class in no.uib.triogen.processing.linear_model">RegressionResult</a></dt>
<dd>
<div class="block">Computes the significance of the model relative to an intercept.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/RegressionResult.html#computeModelSignificance-java.util.HashMap-">computeModelSignificance(HashMap<String, RegressionResult>)</a></span> - Method in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/RegressionResult.html" title="class in no.uib.triogen.processing.linear_model">RegressionResult</a></dt>
<dd>
<div class="block">Computes the model significance against available parent models.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/RegressionResult.html#computeRSS--">computeRSS()</a></span> - Method in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/RegressionResult.html" title="class in no.uib.triogen.processing.linear_model">RegressionResult</a></dt>
<dd>
<div class="block">Sets the residual sum of squares for the given residuals.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/simple_score/SimpleScoreComputer.html#computeScore--">computeScore()</a></span> - Method in class no.uib.triogen.processing.simple_score.<a href="no/uib/triogen/processing/simple_score/SimpleScoreComputer.html" title="class in no.uib.triogen.processing.simple_score">SimpleScoreComputer</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/ld/ComputeTargetedLD.html" title="class in no.uib.triogen.scripts_marc.ld"><span class="typeNameLink">ComputeTargetedLD</span></a> - Class in <a href="no/uib/triogen/scripts_marc/ld/package-summary.html">no.uib.triogen.scripts_marc.ld</a></dt>
<dd>
<div class="block">Debugs the LD calculation.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/ld/ComputeTargetedLD.html#ComputeTargetedLD--">ComputeTargetedLD()</a></span> - Constructor for class no.uib.triogen.scripts_marc.ld.<a href="no/uib/triogen/scripts_marc/ld/ComputeTargetedLD.html" title="class in no.uib.triogen.scripts_marc.ld">ComputeTargetedLD</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/variant_data/BgenVariantTrioData.html#contains-java.lang.String-">contains(String)</a></span> - Method in class no.uib.triogen.io.genotypes.bgen.variant_data.<a href="no/uib/triogen/io/genotypes/bgen/variant_data/BgenVariantTrioData.html" title="class in no.uib.triogen.io.genotypes.bgen.variant_data">BgenVariantTrioData</a></dt>
<dd>
<div class="block">Returns a boolean indicating whether genotyping information is available
for the given sample.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/trio_genotypes/VariantList.html#contains-java.lang.String-">contains(String)</a></span> - Method in class no.uib.triogen.model.trio_genotypes.<a href="no/uib/triogen/model/trio_genotypes/VariantList.html" title="class in no.uib.triogen.model.trio_genotypes">VariantList</a></dt>
<dd>
<div class="block">Returns a boolean indicating whether the variant id is in the list.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/annotation/ensembl/VariantCoordinates.html#contig">contig</a></span> - Variable in class no.uib.triogen.model.annotation.ensembl.<a href="no/uib/triogen/model/annotation/ensembl/VariantCoordinates.html" title="class in no.uib.triogen.model.annotation.ensembl">VariantCoordinates</a></dt>
<dd>
<div class="block">The contig.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/annotation/ProxyCoordinates.html#contig">contig</a></span> - Variable in class no.uib.triogen.model.annotation.<a href="no/uib/triogen/model/annotation/ProxyCoordinates.html" title="class in no.uib.triogen.model.annotation">ProxyCoordinates</a></dt>
<dd>
<div class="block">The contig.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/genome/VariantInformation.html#contig">contig</a></span> - Variable in class no.uib.triogen.model.genome.<a href="no/uib/triogen/model/genome/VariantInformation.html" title="class in no.uib.triogen.model.genome">VariantInformation</a></dt>
<dd>
<div class="block">The contig of the variant.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptionsBean.html#contigColName">contigColName</a></span> - Variable in class no.uib.triogen.cmd.ld_pruning.<a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptionsBean.html" title="class in no.uib.triogen.cmd.ld_pruning">LdPruningOptionsBean</a></dt>
<dd>
<div class="block">The name of the contig column.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/conversion/VcfToBgenConverter.html#convert-java.io.File-java.io.File-">convert(File, File)</a></span> - Method in class no.uib.triogen.io.conversion.<a href="no/uib/triogen/io/conversion/VcfToBgenConverter.html" title="class in no.uib.triogen.io.conversion">VcfToBgenConverter</a></dt>
<dd>
<div class="block">Converts a vcf file to a bgen file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html#covariatesGeneral">covariatesGeneral</a></span> - Variable in class no.uib.triogen.cmd.association.<a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html" title="class in no.uib.triogen.cmd.association">LinearModelOptionsBean</a></dt>
<dd>
<div class="block">Names of the covariates to use for all the phenotypes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_data/VariantDataOptionsBean.html#covariatesGeneral">covariatesGeneral</a></span> - Variable in class no.uib.triogen.cmd.variant_data.<a href="no/uib/triogen/cmd/variant_data/VariantDataOptionsBean.html" title="class in no.uib.triogen.cmd.variant_data">VariantDataOptionsBean</a></dt>
<dd>
<div class="block">Names of the covariates to use for all the phenotypes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/LinearModelComputer.html#covariatesGeneral">covariatesGeneral</a></span> - Variable in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/LinearModelComputer.html" title="class in no.uib.triogen.processing.linear_model">LinearModelComputer</a></dt>
<dd>
<div class="block">Names of the covariates to use for all the phenotypes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/variant_data/VariantDataExtractor.html#covariatesGeneral">covariatesGeneral</a></span> - Variable in class no.uib.triogen.processing.variant_data.<a href="no/uib/triogen/processing/variant_data/VariantDataExtractor.html" title="class in no.uib.triogen.processing.variant_data">VariantDataExtractor</a></dt>
<dd>
<div class="block">Names of the covariates to use for all the phenotypes.</div>
</dd>
<dt><a href="no/uib/triogen/model/covariates/CovariatesHandler.html" title="class in no.uib.triogen.model.covariates"><span class="typeNameLink">CovariatesHandler</span></a> - Class in <a href="no/uib/triogen/model/covariates/package-summary.html">no.uib.triogen.model.covariates</a></dt>
<dd>
<div class="block">Handler for covariates.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/covariates/CovariatesHandler.html#CovariatesHandler-java.lang.String:A-no.uib.triogen.model.phenotypes.PhenotypesHandler-java.lang.String:A-java.util.HashMap-">CovariatesHandler(String[], PhenotypesHandler, String[], HashMap<String, TreeSet<String>>)</a></span> - Constructor for class no.uib.triogen.model.covariates.<a href="no/uib/triogen/model/covariates/CovariatesHandler.html" title="class in no.uib.triogen.model.covariates">CovariatesHandler</a></dt>
<dd>
<div class="block">Constructor.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/covariates/CovariatesHandler.html#covariatesMap">covariatesMap</a></span> - Variable in class no.uib.triogen.model.covariates.<a href="no/uib/triogen/model/covariates/CovariatesHandler.html" title="class in no.uib.triogen.model.covariates">CovariatesHandler</a></dt>
<dd>
<div class="block">Phenotype name to covariates.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html#covariatesSpecific">covariatesSpecific</a></span> - Variable in class no.uib.triogen.cmd.association.<a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html" title="class in no.uib.triogen.cmd.association">LinearModelOptionsBean</a></dt>
<dd>
<div class="block">Map of the covariates to use for specific phenotypes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_data/VariantDataOptionsBean.html#covariatesSpecific">covariatesSpecific</a></span> - Variable in class no.uib.triogen.cmd.variant_data.<a href="no/uib/triogen/cmd/variant_data/VariantDataOptionsBean.html" title="class in no.uib.triogen.cmd.variant_data">VariantDataOptionsBean</a></dt>
<dd>
<div class="block">Map of the covariates to use for specific phenotypes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/linear_model/LinearModelComputer.html#covariatesSpecific">covariatesSpecific</a></span> - Variable in class no.uib.triogen.processing.linear_model.<a href="no/uib/triogen/processing/linear_model/LinearModelComputer.html" title="class in no.uib.triogen.processing.linear_model">LinearModelComputer</a></dt>
<dd>
<div class="block">Map of the covariates to use for specific phenotypes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/variant_data/VariantDataExtractor.html#covariatesSpecific">covariatesSpecific</a></span> - Variable in class no.uib.triogen.processing.variant_data.<a href="no/uib/triogen/processing/variant_data/VariantDataExtractor.html" title="class in no.uib.triogen.processing.variant_data">VariantDataExtractor</a></dt>
<dd>
<div class="block">Map of the covariates to use for specific phenotypes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/association/LinearModelOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.association.<a href="no/uib/triogen/cmd/association/LinearModelOptions.html" title="enum in no.uib.triogen.cmd.association">LinearModelOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/extract/ExtractOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.extract.<a href="no/uib/triogen/cmd/extract/ExtractOptions.html" title="enum in no.uib.triogen.cmd.extract">ExtractOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.ld_matrix.<a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptions.html" title="enum in no.uib.triogen.cmd.ld_matrix">LdMatrixOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.ld_pruning.<a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptions.html" title="enum in no.uib.triogen.cmd.ld_pruning">LdPruningOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_value/LdValueOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.ld_value.<a href="no/uib/triogen/cmd/ld_value/LdValueOptions.html" title="enum in no.uib.triogen.cmd.ld_value">LdValueOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/locus/LocusZoomOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.locus.<a href="no/uib/triogen/cmd/locus/LocusZoomOptions.html" title="enum in no.uib.triogen.cmd.locus">LocusZoomOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.mendelian_check.<a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptions.html" title="enum in no.uib.triogen.cmd.mendelian_check">MendelianCheckOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.prs_prune.<a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptions.html" title="enum in no.uib.triogen.cmd.prs_prune">PrsPruneOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_score/PrsScoreOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.prs_score.<a href="no/uib/triogen/cmd/prs_score/PrsScoreOptions.html" title="enum in no.uib.triogen.cmd.prs_score">PrsScoreOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.prs_threshold.<a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptions.html" title="enum in no.uib.triogen.cmd.prs_threshold">PrsThresholdOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/simple_score/SimpleScoreOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.simple_score.<a href="no/uib/triogen/cmd/simple_score/SimpleScoreOptions.html" title="enum in no.uib.triogen.cmd.simple_score">SimpleScoreOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_data/VariantDataOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.variant_data.<a href="no/uib/triogen/cmd/variant_data/VariantDataOptions.html" title="enum in no.uib.triogen.cmd.variant_data">VariantDataOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_file/VariantFileOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.variant_file.<a href="no/uib/triogen/cmd/variant_file/VariantFileOptions.html" title="enum in no.uib.triogen.cmd.variant_file">VariantFileOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/vcf_to_bgen/VcfToBgenOptions.html#createOptionsCLI-org.apache.commons.cli.Options-">createOptionsCLI(Options)</a></span> - Static method in enum no.uib.triogen.cmd.vcf_to_bgen.<a href="no/uib/triogen/cmd/vcf_to_bgen/VcfToBgenOptions.html" title="enum in no.uib.triogen.cmd.vcf_to_bgen">VcfToBgenOptions</a></dt>
<dd>
<div class="block">Creates the options for the command line interface based on the possible
values.</div>
</dd>
</dl>
<a name="I:D">
<!-- -->
</a>
<h2 class="title">D</h2>
<dl>
<dt><a href="no/uib/triogen/scripts_marc/ld/DebugLd.html" title="class in no.uib.triogen.scripts_marc.ld"><span class="typeNameLink">DebugLd</span></a> - Class in <a href="no/uib/triogen/scripts_marc/ld/package-summary.html">no.uib.triogen.scripts_marc.ld</a></dt>
<dd>
<div class="block">Debugs the LD calculation.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/ld/DebugLd.html#DebugLd--">DebugLd()</a></span> - Constructor for class no.uib.triogen.scripts_marc.ld.<a href="no/uib/triogen/scripts_marc/ld/DebugLd.html" title="class in no.uib.triogen.scripts_marc.ld">DebugLd</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/InheritanceUtils.html#DEFAULT_CHROMOSOME_INHERITANCE_MAP">DEFAULT_CHROMOSOME_INHERITANCE_MAP</a></span> - Static variable in class no.uib.triogen.io.genotypes.<a href="no/uib/triogen/io/genotypes/InheritanceUtils.html" title="class in no.uib.triogen.io.genotypes">InheritanceUtils</a></dt>
<dd>
<div class="block">The default chromosome inheritance map for children.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/annotation/ensembl/EnsemblAPI.html#DELAY">DELAY</a></span> - Static variable in class no.uib.triogen.model.annotation.ensembl.<a href="no/uib/triogen/model/annotation/ensembl/EnsemblAPI.html" title="class in no.uib.triogen.model.annotation.ensembl">EnsemblAPI</a></dt>
<dd>
<div class="block">The delay between attempts.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/annotation/ld_link/LDproxy.html#DELAY">DELAY</a></span> - Static variable in class no.uib.triogen.model.annotation.ld_link.<a href="no/uib/triogen/model/annotation/ld_link/LDproxy.html" title="class in no.uib.triogen.model.annotation.ld_link">LDproxy</a></dt>
<dd>
<div class="block">The delay between attempts.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/SimpleTimeSemaphore.html#delay--">delay()</a></span> - Method in class no.uib.triogen.utils.<a href="no/uib/triogen/utils/SimpleTimeSemaphore.html" title="class in no.uib.triogen.utils">SimpleTimeSemaphore</a></dt>
<dd>
<div class="block">Delays of the</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/utils/Waiter.html#delay-long-">delay(long)</a></span> - Method in class no.uib.triogen.utils.<a href="no/uib/triogen/utils/Waiter.html" title="class in no.uib.triogen.utils">Waiter</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/association/LinearModelOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.association.<a href="no/uib/triogen/cmd/association/LinearModelOptions.html" title="enum in no.uib.triogen.cmd.association">LinearModelOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/extract/ExtractOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.extract.<a href="no/uib/triogen/cmd/extract/ExtractOptions.html" title="enum in no.uib.triogen.cmd.extract">ExtractOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.ld_matrix.<a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptions.html" title="enum in no.uib.triogen.cmd.ld_matrix">LdMatrixOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.ld_pruning.<a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptions.html" title="enum in no.uib.triogen.cmd.ld_pruning">LdPruningOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_value/LdValueOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.ld_value.<a href="no/uib/triogen/cmd/ld_value/LdValueOptions.html" title="enum in no.uib.triogen.cmd.ld_value">LdValueOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/locus/LocusZoomOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.locus.<a href="no/uib/triogen/cmd/locus/LocusZoomOptions.html" title="enum in no.uib.triogen.cmd.locus">LocusZoomOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.mendelian_check.<a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptions.html" title="enum in no.uib.triogen.cmd.mendelian_check">MendelianCheckOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.prs_prune.<a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptions.html" title="enum in no.uib.triogen.cmd.prs_prune">PrsPruneOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_score/PrsScoreOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.prs_score.<a href="no/uib/triogen/cmd/prs_score/PrsScoreOptions.html" title="enum in no.uib.triogen.cmd.prs_score">PrsScoreOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.prs_threshold.<a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptions.html" title="enum in no.uib.triogen.cmd.prs_threshold">PrsThresholdOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/simple_score/SimpleScoreOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.simple_score.<a href="no/uib/triogen/cmd/simple_score/SimpleScoreOptions.html" title="enum in no.uib.triogen.cmd.simple_score">SimpleScoreOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_data/VariantDataOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.variant_data.<a href="no/uib/triogen/cmd/variant_data/VariantDataOptions.html" title="enum in no.uib.triogen.cmd.variant_data">VariantDataOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_file/VariantFileOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.variant_file.<a href="no/uib/triogen/cmd/variant_file/VariantFileOptions.html" title="enum in no.uib.triogen.cmd.variant_file">VariantFileOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/vcf_to_bgen/VcfToBgenOptions.html#description">description</a></span> - Variable in enum no.uib.triogen.cmd.vcf_to_bgen.<a href="no/uib/triogen/cmd/vcf_to_bgen/VcfToBgenOptions.html" title="enum in no.uib.triogen.cmd.vcf_to_bgen">VcfToBgenOptions</a></dt>
<dd>
<div class="block">Explanation for the CLI option.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/trio_genotypes/Model.html#description">description</a></span> - Variable in enum no.uib.triogen.model.trio_genotypes.<a href="no/uib/triogen/model/trio_genotypes/Model.html" title="enum in no.uib.triogen.model.trio_genotypes">Model</a></dt>
<dd>
<div class="block">The description of the model.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html#destinationFile">destinationFile</a></span> - Variable in class no.uib.triogen.cmd.association.<a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html" title="class in no.uib.triogen.cmd.association">LinearModelOptionsBean</a></dt>
<dd>
<div class="block">The file where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptionsBean.html#destinationFile">destinationFile</a></span> - Variable in class no.uib.triogen.cmd.ld_pruning.<a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptionsBean.html" title="class in no.uib.triogen.cmd.ld_pruning">LdPruningOptionsBean</a></dt>
<dd>
<div class="block">File where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_value/LdValueOptionsBean.html#destinationFile">destinationFile</a></span> - Variable in class no.uib.triogen.cmd.ld_value.<a href="no/uib/triogen/cmd/ld_value/LdValueOptionsBean.html" title="class in no.uib.triogen.cmd.ld_value">LdValueOptionsBean</a></dt>
<dd>
<div class="block">File where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptionsBean.html#destinationFile">destinationFile</a></span> - Variable in class no.uib.triogen.cmd.mendelian_check.<a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptionsBean.html" title="class in no.uib.triogen.cmd.mendelian_check">MendelianCheckOptionsBean</a></dt>
<dd>
<div class="block">File where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html#destinationFile">destinationFile</a></span> - Variable in class no.uib.triogen.cmd.prs_prune.<a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html" title="class in no.uib.triogen.cmd.prs_prune">PrsPruneOptionsBean</a></dt>
<dd>
<div class="block">The file where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html#destinationFile">destinationFile</a></span> - Variable in class no.uib.triogen.cmd.prs_score.<a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html" title="class in no.uib.triogen.cmd.prs_score">PrsScoreOptionsBean</a></dt>
<dd>
<div class="block">The file where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html#destinationFile">destinationFile</a></span> - Variable in class no.uib.triogen.cmd.prs_threshold.<a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html" title="class in no.uib.triogen.cmd.prs_threshold">PrsThresholdOptionsBean</a></dt>
<dd>
<div class="block">The file where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/simple_score/SimpleScoreOptionsBean.html#destinationFile">destinationFile</a></span> - Variable in class no.uib.triogen.cmd.simple_score.<a href="no/uib/triogen/cmd/simple_score/SimpleScoreOptionsBean.html" title="class in no.uib.triogen.cmd.simple_score">SimpleScoreOptionsBean</a></dt>
<dd>
<div class="block">The file where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_data/VariantDataOptionsBean.html#destinationFile">destinationFile</a></span> - Variable in class no.uib.triogen.cmd.variant_data.<a href="no/uib/triogen/cmd/variant_data/VariantDataOptionsBean.html" title="class in no.uib.triogen.cmd.variant_data">VariantDataOptionsBean</a></dt>
<dd>
<div class="block">The file where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_file/VariantFileOptionsBean.html#destinationFile">destinationFile</a></span> - Variable in class no.uib.triogen.cmd.variant_file.<a href="no/uib/triogen/cmd/variant_file/VariantFileOptionsBean.html" title="class in no.uib.triogen.cmd.variant_file">VariantFileOptionsBean</a></dt>
<dd>
<div class="block">The file where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptionsBean.html#destinationFilePath">destinationFilePath</a></span> - Variable in class no.uib.triogen.cmd.ld_matrix.<a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptionsBean.html" title="class in no.uib.triogen.cmd.ld_matrix">LdMatrixOptionsBean</a></dt>
<dd>
<div class="block">File where to write the output.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/vcf/reader/VcfVariant.html#DOSAGE_KEY">DOSAGE_KEY</a></span> - Static variable in class no.uib.triogen.io.genotypes.vcf.reader.<a href="no/uib/triogen/io/genotypes/vcf/reader/VcfVariant.html" title="class in no.uib.triogen.io.genotypes.vcf.reader">VcfVariant</a></dt>
<dd>
<div class="block">Vcf key for the dosages.</div>
</dd>
</dl>
<a name="I:E">
<!-- -->
</a>
<h2 class="title">E</h2>
<dl>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html#eaColumn">eaColumn</a></span> - Variable in class no.uib.triogen.cmd.prs_prune.<a href="no/uib/triogen/cmd/prs_prune/PrsPruneOptionsBean.html" title="class in no.uib.triogen.cmd.prs_prune">PrsPruneOptionsBean</a></dt>
<dd>
<div class="block">Name of the effect allele column in the training file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/simple_score/VariantWeightList.html#effectAllele">effectAllele</a></span> - Variable in class no.uib.triogen.model.simple_score.<a href="no/uib/triogen/model/simple_score/VariantWeightList.html" title="class in no.uib.triogen.model.simple_score">VariantWeightList</a></dt>
<dd>
<div class="block">The effect alleles.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/vcf/reader/VcfVariant.html#emptyGenotypeDosageCaches--">emptyGenotypeDosageCaches()</a></span> - Method in class no.uib.triogen.io.genotypes.vcf.reader.<a href="no/uib/triogen/io/genotypes/vcf/reader/VcfVariant.html" title="class in no.uib.triogen.io.genotypes.vcf.reader">VcfVariant</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/IoUtils.html#ENCODING">ENCODING</a></span> - Static variable in class no.uib.triogen.io.<a href="no/uib/triogen/io/IoUtils.html" title="class in no.uib.triogen.io">IoUtils</a></dt>
<dd>
<div class="block">Default encoding, cf the second rule.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/annotation/ensembl/GeneCoordinates.html#end">end</a></span> - Variable in class no.uib.triogen.model.annotation.ensembl.<a href="no/uib/triogen/model/annotation/ensembl/GeneCoordinates.html" title="class in no.uib.triogen.model.annotation.ensembl">GeneCoordinates</a></dt>
<dd>
<div class="block">The end position.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/annotation/ProxyCoordinates.html#end">end</a></span> - Variable in class no.uib.triogen.model.annotation.<a href="no/uib/triogen/model/annotation/ProxyCoordinates.html" title="class in no.uib.triogen.model.annotation">ProxyCoordinates</a></dt>
<dd>
<div class="block">The end position.</div>
</dd>
<dt><a href="no/uib/triogen/model/annotation/ensembl/EnsemblAPI.html" title="class in no.uib.triogen.model.annotation.ensembl"><span class="typeNameLink">EnsemblAPI</span></a> - Class in <a href="no/uib/triogen/model/annotation/ensembl/package-summary.html">no.uib.triogen.model.annotation.ensembl</a></dt>
<dd>
<div class="block">This class allows retrieving information from the Ensembl API.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/annotation/ensembl/EnsemblAPI.html#EnsemblAPI--">EnsemblAPI()</a></span> - Constructor for class no.uib.triogen.model.annotation.ensembl.<a href="no/uib/triogen/model/annotation/ensembl/EnsemblAPI.html" title="class in no.uib.triogen.model.annotation.ensembl">EnsemblAPI</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptionsBean.html#ensemblPopulation">ensemblPopulation</a></span> - Variable in class no.uib.triogen.cmd.ld_pruning.<a href="no/uib/triogen/cmd/ld_pruning/LdPruningOptionsBean.html" title="class in no.uib.triogen.cmd.ld_pruning">LdPruningOptionsBean</a></dt>
<dd>
<div class="block">The reference population to use for Ensembl.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_file/VariantFileOptionsBean.html#ensemblPopulation">ensemblPopulation</a></span> - Variable in class no.uib.triogen.cmd.variant_file.<a href="no/uib/triogen/cmd/variant_file/VariantFileOptionsBean.html" title="class in no.uib.triogen.cmd.variant_file">VariantFileOptionsBean</a></dt>
<dd>
<div class="block">The reference population to use for Ensembl.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/trio_genotypes/Model.html#equation">equation</a></span> - Variable in enum no.uib.triogen.model.trio_genotypes.<a href="no/uib/triogen/model/trio_genotypes/Model.html" title="enum in no.uib.triogen.model.trio_genotypes">Model</a></dt>
<dd>
<div class="block">The equation of the model.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/mendelian_error/MendelianErrorEstimator.html#estimateMendelianErrorPrevalence-no.uib.triogen.io.genotypes.bgen.variant_data.BgenVariantTrioData-no.uib.triogen.model.family.ChildToParentMap-int-">estimateMendelianErrorPrevalence(BgenVariantTrioData, ChildToParentMap, int)</a></span> - Static method in class no.uib.triogen.model.mendelian_error.<a href="no/uib/triogen/model/mendelian_error/MendelianErrorEstimator.html" title="class in no.uib.triogen.model.mendelian_error">MendelianErrorEstimator</a></dt>
<dd>
<div class="block">Estimates the prevalence of Mendelian errors by comparing the number of
001*, *100, 110*, *011 resulting in +2 or -1 tested alleles for the
parents compared to the number of such trios expected according to the
maf.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/processing/ld/LdMatrixComputerRunnable.html#EXCLUDED_VARIANTS_CACHE_SIZE">EXCLUDED_VARIANTS_CACHE_SIZE</a></span> - Static variable in class no.uib.triogen.processing.ld.<a href="no/uib/triogen/processing/ld/LdMatrixComputerRunnable.html" title="class in no.uib.triogen.processing.ld">LdMatrixComputerRunnable</a></dt>
<dd>
<div class="block">The size of the cache for excluded variants.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/ld/LdMatrixUtils.html#EXTENSION">EXTENSION</a></span> - Static variable in class no.uib.triogen.io.ld.<a href="no/uib/triogen/io/ld/LdMatrixUtils.html" title="class in no.uib.triogen.io.ld">LdMatrixUtils</a></dt>
<dd>
<div class="block">The file extension.</div>
</dd>
<dt><a href="no/uib/triogen/cmd/extract/Extract.html" title="class in no.uib.triogen.cmd.extract"><span class="typeNameLink">Extract</span></a> - Class in <a href="no/uib/triogen/cmd/extract/package-summary.html">no.uib.triogen.cmd.extract</a></dt>
<dd>
<div class="block">Runs multiple linear models for the association with phenotypes.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/extract/Extract.html#Extract--">Extract()</a></span> - Constructor for class no.uib.triogen.cmd.extract.<a href="no/uib/triogen/cmd/extract/Extract.html" title="class in no.uib.triogen.cmd.extract">Extract</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/bolt/ExtractBolt.html" title="class in no.uib.triogen.scripts_marc.bolt"><span class="typeNameLink">ExtractBolt</span></a> - Class in <a href="no/uib/triogen/scripts_marc/bolt/package-summary.html">no.uib.triogen.scripts_marc.bolt</a></dt>
<dd>
<div class="block">Extracts variants from bolt files around a set of targets.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/bolt/ExtractBolt.html#ExtractBolt--">ExtractBolt()</a></span> - Constructor for class no.uib.triogen.scripts_marc.bolt.<a href="no/uib/triogen/scripts_marc/bolt/ExtractBolt.html" title="class in no.uib.triogen.scripts_marc.bolt">ExtractBolt</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/vcf/ExtractFromVcf.html" title="class in no.uib.triogen.scripts_marc.vcf"><span class="typeNameLink">ExtractFromVcf</span></a> - Class in <a href="no/uib/triogen/scripts_marc/vcf/package-summary.html">no.uib.triogen.scripts_marc.vcf</a></dt>
<dd>
<div class="block">Extract data from vcf files.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/vcf/ExtractFromVcf.html#ExtractFromVcf--">ExtractFromVcf()</a></span> - Constructor for class no.uib.triogen.scripts_marc.vcf.<a href="no/uib/triogen/scripts_marc/vcf/ExtractFromVcf.html" title="class in no.uib.triogen.scripts_marc.vcf">ExtractFromVcf</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/ld/ComputeTargetedLD.html#extractLD-java.lang.String-java.io.File-no.uib.triogen.model.family.ChildToParentMap-">extractLD(String, File, ChildToParentMap)</a></span> - Static method in class no.uib.triogen.scripts_marc.ld.<a href="no/uib/triogen/scripts_marc/ld/ComputeTargetedLD.html" title="class in no.uib.triogen.scripts_marc.ld">ComputeTargetedLD</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/ld/ComputeTargetedLD.html#extractLD-java.lang.String-java.lang.String-no.uib.triogen.io.genotypes.bgen.index.BgenIndex-no.uib.triogen.io.genotypes.bgen.reader.BgenFileReader-no.uib.triogen.model.family.ChildToParentMap-">extractLD(String, String, BgenIndex, BgenFileReader, ChildToParentMap)</a></span> - Static method in class no.uib.triogen.scripts_marc.ld.<a href="no/uib/triogen/scripts_marc/ld/ComputeTargetedLD.html" title="class in no.uib.triogen.scripts_marc.ld">ComputeTargetedLD</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/ld/ExtractLd.html" title="class in no.uib.triogen.scripts_marc.ld"><span class="typeNameLink">ExtractLd</span></a> - Class in <a href="no/uib/triogen/scripts_marc/ld/package-summary.html">no.uib.triogen.scripts_marc.ld</a></dt>
<dd>
<div class="block">Extracts specific lines of a file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/ld/ExtractLd.html#ExtractLd--">ExtractLd()</a></span> - Constructor for class no.uib.triogen.scripts_marc.ld.<a href="no/uib/triogen/scripts_marc/ld/ExtractLd.html" title="class in no.uib.triogen.scripts_marc.ld">ExtractLd</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/scripts_marc/misc/ExtractNs.html" title="class in no.uib.triogen.scripts_marc.misc"><span class="typeNameLink">ExtractNs</span></a> - Class in <a href="no/uib/triogen/scripts_marc/misc/package-summary.html">no.uib.triogen.scripts_marc.misc</a></dt>
<dd>
<div class="block">This scripts extracts the number of samples with given genotypes for each
variant.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/misc/ExtractNs.html#ExtractNs--">ExtractNs()</a></span> - Constructor for class no.uib.triogen.scripts_marc.misc.<a href="no/uib/triogen/scripts_marc/misc/ExtractNs.html" title="class in no.uib.triogen.scripts_marc.misc">ExtractNs</a></dt>
<dd> </dd>
<dt><a href="no/uib/triogen/cmd/extract/ExtractOptions.html" title="enum in no.uib.triogen.cmd.extract"><span class="typeNameLink">ExtractOptions</span></a> - Enum in <a href="no/uib/triogen/cmd/extract/package-summary.html">no.uib.triogen.cmd.extract</a></dt>
<dd>
<div class="block">Enum of the different options</div>
</dd>
<dt><a href="no/uib/triogen/cmd/extract/ExtractOptionsBean.html" title="class in no.uib.triogen.cmd.extract"><span class="typeNameLink">ExtractOptionsBean</span></a> - Class in <a href="no/uib/triogen/cmd/extract/package-summary.html">no.uib.triogen.cmd.extract</a></dt>
<dd>
<div class="block">Parses and stores the command line options.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/extract/ExtractOptionsBean.html#ExtractOptionsBean-org.apache.commons.cli.CommandLine-">ExtractOptionsBean(CommandLine)</a></span> - Constructor for class no.uib.triogen.cmd.extract.<a href="no/uib/triogen/cmd/extract/ExtractOptionsBean.html" title="class in no.uib.triogen.cmd.extract">ExtractOptionsBean</a></dt>
<dd>
<div class="block">Constructor.</div>
</dd>
</dl>
<a name="I:F">
<!-- -->
</a>
<h2 class="title">F</h2>
<dl>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/InheritanceUtils.html#FATHER">FATHER</a></span> - Static variable in class no.uib.triogen.io.genotypes.<a href="no/uib/triogen/io/genotypes/InheritanceUtils.html" title="class in no.uib.triogen.io.genotypes">InheritanceUtils</a></dt>
<dd>
<div class="block">The key for fathers.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/writer/BgenWriter.html#finalize--">finalize()</a></span> - Method in class no.uib.triogen.io.genotypes.bgen.writer.<a href="no/uib/triogen/io/genotypes/bgen/writer/BgenWriter.html" title="class in no.uib.triogen.io.genotypes.bgen.writer">BgenWriter</a></dt>
<dd>
<div class="block">Finalizes the file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/bgen/index/BgenIndex.html#FIRST_LINE">FIRST_LINE</a></span> - Static variable in class no.uib.triogen.io.genotypes.bgen.index.<a href="no/uib/triogen/io/genotypes/bgen/index/BgenIndex.html" title="class in no.uib.triogen.io.genotypes.bgen.index">BgenIndex</a></dt>
<dd>
<div class="block">The first line of the index.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/family/ChildToParentMap.html#fromFile-java.io.File-">fromFile(File)</a></span> - Static method in class no.uib.triogen.model.family.<a href="no/uib/triogen/model/family/ChildToParentMap.html" title="class in no.uib.triogen.model.family">ChildToParentMap</a></dt>
<dd>
<div class="block">Parses the trio map from a file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/trio_genotypes/Model.html#fullName">fullName</a></span> - Variable in enum no.uib.triogen.model.trio_genotypes.<a href="no/uib/triogen/model/trio_genotypes/Model.html" title="enum in no.uib.triogen.model.trio_genotypes">Model</a></dt>
<dd>
<div class="block">The full name of the model.</div>
</dd>
</dl>
<a name="I:G">
<!-- -->
</a>
<h2 class="title">G</h2>
<dl>
<dt><a href="no/uib/triogen/model/annotation/ensembl/GeneCoordinates.html" title="class in no.uib.triogen.model.annotation.ensembl"><span class="typeNameLink">GeneCoordinates</span></a> - Class in <a href="no/uib/triogen/model/annotation/ensembl/package-summary.html">no.uib.triogen.model.annotation.ensembl</a></dt>
<dd>
<div class="block">Gene coordinates as retrieved from the Ensembl API.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/model/annotation/ensembl/GeneCoordinates.html#GeneCoordinates-java.lang.String-java.lang.String-int-int-">GeneCoordinates(String, String, int, int)</a></span> - Constructor for class no.uib.triogen.model.annotation.ensembl.<a href="no/uib/triogen/model/annotation/ensembl/GeneCoordinates.html" title="class in no.uib.triogen.model.annotation.ensembl">GeneCoordinates</a></dt>
<dd>
<div class="block">Constructor.</div>
</dd>
<dt><a href="no/uib/triogen/scripts_marc/ensembl/GeneCoordinates.html" title="class in no.uib.triogen.scripts_marc.ensembl"><span class="typeNameLink">GeneCoordinates</span></a> - Class in <a href="no/uib/triogen/scripts_marc/ensembl/package-summary.html">no.uib.triogen.scripts_marc.ensembl</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/scripts_marc/ensembl/GeneCoordinates.html#GeneCoordinates--">GeneCoordinates()</a></span> - Constructor for class no.uib.triogen.scripts_marc.ensembl.<a href="no/uib/triogen/scripts_marc/ensembl/GeneCoordinates.html" title="class in no.uib.triogen.scripts_marc.ensembl">GeneCoordinates</a></dt>
<dd> </dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/locus/LocusZoomOptionsBean.html#geneCoordinatesFileStem">geneCoordinatesFileStem</a></span> - Variable in class no.uib.triogen.cmd.locus.<a href="no/uib/triogen/cmd/locus/LocusZoomOptionsBean.html" title="class in no.uib.triogen.cmd.locus">LocusZoomOptionsBean</a></dt>
<dd>
<div class="block">Stem for the gene coordinates file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/genotypes/vcf/reader/VcfVariant.html#genotyped--">genotyped()</a></span> - Method in class no.uib.triogen.io.genotypes.vcf.reader.<a href="no/uib/triogen/io/genotypes/vcf/reader/VcfVariant.html" title="class in no.uib.triogen.io.genotypes.vcf.reader">VcfVariant</a></dt>
<dd>
<div class="block">Returns a boolean indicating whether the variant is genotyped.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html#genotypesFile">genotypesFile</a></span> - Variable in class no.uib.triogen.cmd.association.<a href="no/uib/triogen/cmd/association/LinearModelOptionsBean.html" title="class in no.uib.triogen.cmd.association">LinearModelOptionsBean</a></dt>
<dd>
<div class="block">The genotypes file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptionsBean.html#genotypesFile">genotypesFile</a></span> - Variable in class no.uib.triogen.cmd.ld_matrix.<a href="no/uib/triogen/cmd/ld_matrix/LdMatrixOptionsBean.html" title="class in no.uib.triogen.cmd.ld_matrix">LdMatrixOptionsBean</a></dt>
<dd>
<div class="block">The genotypes file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptionsBean.html#genotypesFile">genotypesFile</a></span> - Variable in class no.uib.triogen.cmd.mendelian_check.<a href="no/uib/triogen/cmd/mendelian_check/MendelianCheckOptionsBean.html" title="class in no.uib.triogen.cmd.mendelian_check">MendelianCheckOptionsBean</a></dt>
<dd>
<div class="block">The genotypes file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html#genotypesFile">genotypesFile</a></span> - Variable in class no.uib.triogen.cmd.prs_score.<a href="no/uib/triogen/cmd/prs_score/PrsScoreOptionsBean.html" title="class in no.uib.triogen.cmd.prs_score">PrsScoreOptionsBean</a></dt>
<dd>
<div class="block">The genotypes file path.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html#genotypesFile">genotypesFile</a></span> - Variable in class no.uib.triogen.cmd.prs_threshold.<a href="no/uib/triogen/cmd/prs_threshold/PrsThresholdOptionsBean.html" title="class in no.uib.triogen.cmd.prs_threshold">PrsThresholdOptionsBean</a></dt>
<dd>
<div class="block">The genotypes file path.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/simple_score/SimpleScoreOptionsBean.html#genotypesFile">genotypesFile</a></span> - Variable in class no.uib.triogen.cmd.simple_score.<a href="no/uib/triogen/cmd/simple_score/SimpleScoreOptionsBean.html" title="class in no.uib.triogen.cmd.simple_score">SimpleScoreOptionsBean</a></dt>
<dd>
<div class="block">The genotypes file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_data/VariantDataOptionsBean.html#genotypesFile">genotypesFile</a></span> - Variable in class no.uib.triogen.cmd.variant_data.<a href="no/uib/triogen/cmd/variant_data/VariantDataOptionsBean.html" title="class in no.uib.triogen.cmd.variant_data">VariantDataOptionsBean</a></dt>
<dd>
<div class="block">The genotypes file.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/cmd/variant_file/VariantFileOptionsBean.html#genotypesFilePath">genotypesFilePath</a></span> - Variable in class no.uib.triogen.cmd.variant_file.<a href="no/uib/triogen/cmd/variant_file/VariantFileOptionsBean.html" title="class in no.uib.triogen.cmd.variant_file">VariantFileOptionsBean</a></dt>
<dd>
<div class="block">The path to the genotypes file with chromosome encoded.</div>
</dd>
<dt><span class="memberNameLink"><a href="no/uib/triogen/io/flat/mapping/MemoryMappedFile.MiniBuffer.html#get-byte:A-">get(byte[])</a></span> - Method in class no.uib.triogen.io.flat.mapping.<a href="no/uib/triogen/io/flat/mapping/MemoryMappedFile.MiniBuffer.html" title="class in no.uib.triogen.io.flat.mapping">MemoryMappedFile.MiniBuffer</a></dt>
<dd>