Removed gelitext package (deprecated)

src/main/java/htsjdk/tribble/example/CountRecords.java

@@ -29,7 +29,6 @@
 import htsjdk.tribble.FeatureCodec;
 import htsjdk.tribble.Tribble;
 import htsjdk.tribble.bed.BEDCodec;
-import htsjdk.tribble.gelitext.GeliTextCodec;
 import htsjdk.tribble.index.Index;
 import htsjdk.tribble.index.IndexFactory;
 import htsjdk.tribble.index.linear.LinearIndex;
@@ -193,8 +192,6 @@ public static FeatureCodec getFeatureCodec(File featureFile) {
         //    return new VCFCodec();
         if (featureFile.getName().endsWith(".bed") || featureFile.getName().endsWith(".BED") )
             return new BEDCodec();
-        if (featureFile.getName().endsWith(".geli.calls") || featureFile.getName().endsWith(".geli") )
-            return new GeliTextCodec();
         throw new IllegalArgumentException("Unable to determine correct file type based on the file name, for file -> " + featureFile);
     }
 }

src/main/java/htsjdk/tribble/gelitext/DiploidGenotype.java

@@ -1,66 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2013 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-package htsjdk.tribble.gelitext;
-
-
-/**
- * Class DiploidGenotype
- *
- * Enum describing all possible combinations of diploid genotype variations;
- * AA, AC, etc.
- *
- * @author aaron
- */
-@Deprecated
-public enum DiploidGenotype {
-    AA, AC, AG, AT, CC, CG, CT, GG, GT, TT;
-
-    public static DiploidGenotype toDiploidGenotype(String genotype) {
-        if (genotype.length() != 2)
-            throw new DiploidGenotypeException("Genotype string for conversion should be of length 2, we were passed = " + genotype);
-        genotype = genotype.toUpperCase();
-        for (DiploidGenotype g: DiploidGenotype.values())
-            if (g.toString().equals(genotype)) return g;
-        throw new DiploidGenotypeException("Unable to find genotype matching " + genotype);
-    }
-
-    public boolean isHet() {
-        return toString().toCharArray()[0] != toString().toCharArray()[1];
-    }
-
-    public boolean containsBase(char base) {
-        return (toString().charAt(0) == base || toString().charAt(1) == base);
-    }
-}
-
-@Deprecated
-class DiploidGenotypeException extends RuntimeException {
-    DiploidGenotypeException(String s) {
-        super(s);
-    }
-
-    DiploidGenotypeException(String s, Throwable throwable) {
-        super(s, throwable);
-    }
-}

src/main/java/htsjdk/tribble/gelitext/GeliTextCodec.java

@@ -1,117 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2013 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-package htsjdk.tribble.gelitext;
-
-import htsjdk.samtools.util.CollectionUtil;
-import htsjdk.tribble.AsciiFeatureCodec;
-import htsjdk.tribble.Feature;
-import htsjdk.tribble.exception.CodecLineParsingException;
-import htsjdk.tribble.readers.LineIterator;
-
-import java.util.Arrays;
-
-
-/**
- * <p/>
- * A codec for parsing geli text files, which is the text version of the geli binary format.
- * <p/>
- * <p/>
- * GELI text has the following tab-seperated fields:
- * contig             the contig (string)
- * position           the position on the contig (long)
- * refBase            the reference base (char)
- * depthOfCoverage    the depth of coverage at this position (int)
- * maximumMappingQual the maximum mapping quality of a read at this position (int)
- * genotype           the called genotype (string)
- * LODBestToReference the LOD score of the best to the reference (double)
- * LODBestToNext      the LOD score of the best to the next best genotype (double)
- * likelihoods        the array of all genotype likelihoods, in ordinal ordering (array of 10 doubles, in ordinal order)
- *
- * @author aaron
- * @deprecated This is deprecated and unsupported.
- */
-@Deprecated
-public class GeliTextCodec extends AsciiFeatureCodec<GeliTextFeature> {
-    public GeliTextCodec() {
-        super(GeliTextFeature.class);
-    }
-
-    public Feature decodeLoc(final String line) {
-        return decode(line);
-    }
-
-    @Override
-    public GeliTextFeature decode(final String line) {
-        // clean out header lines and comments
-        if (line.startsWith("#") || line.startsWith("@"))
-            return null;
-
-        // parse into tokens
-        final String[] parts = line.trim().split("\\s+");
-        return decode(parts);
-    }
-
-    @Override
-    public boolean canDecode(String path){
-	return path.toLowerCase().endsWith(".geli.calls") || path.toLowerCase().endsWith(".geli");
-    }
-
-    @Override
-    public Object readActualHeader(LineIterator reader) {
-        return null;
-    }
-
-    public GeliTextFeature decode(final String[] tokens) {
-        try {
-            // check that we got the correct number of tokens in the split
-            if (tokens.length != 18)
-                throw new CodecLineParsingException("Invalid GeliTextFeature row found -- incorrect element count.  Expected 18, got " + tokens.length + " line = " + CollectionUtil.join(Arrays.asList(tokens), " "));
-
-            // UPPER case and sort
-            final char[] x = tokens[5].toUpperCase().toCharArray();
-            Arrays.sort(x);
-            final String bestGenotype = new String(x);
-
-            final double[] genotypeLikelihoods = new double[10];
-            for (int pieceIndex = 8, offset = 0; pieceIndex < 18; pieceIndex++, offset++) {
-                genotypeLikelihoods[offset] = Double.valueOf(tokens[pieceIndex]);
-            }
-            return new GeliTextFeature(tokens[0],
-                    Long.valueOf(tokens[1]),
-                    Character.toUpperCase(tokens[2].charAt(0)),
-                    Integer.valueOf(tokens[3]),
-                    Integer.valueOf(tokens[4]),
-                    DiploidGenotype.toDiploidGenotype(bestGenotype),
-                    Double.valueOf(tokens[6]),
-                    Double.valueOf(tokens[7]),
-                    genotypeLikelihoods);
-        } catch (CodecLineParsingException e) {
-            e.printStackTrace();
-            throw new RuntimeException("Unable to parse line " + CollectionUtil.join(Arrays.asList(tokens), " "), e);
-        } catch (NumberFormatException e) {
-            e.printStackTrace();
-            throw new RuntimeException("Unable to parse line " + CollectionUtil.join(Arrays.asList(tokens), " "), e);
-        }
-    }
-}

src/main/java/htsjdk/tribble/gelitext/GeliTextFeature.java

@@ -1,148 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2013 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-package htsjdk.tribble.gelitext;
-
-import htsjdk.tribble.Feature;
-
-import java.util.Arrays;
-
-
-/**
- *         <p/>
- *         Class GeliTextFeature
- *         <p/>
- *         This is a feature for the Geli text object, which is the text version of the Geli binary genotyping format.
- *
- * @author aaron
- * @deprecated this is deprecated and no longer supported
- */
-@Deprecated
-public class GeliTextFeature implements Feature {
-
-    private final String contig;                // the contig name
-    private final long position;                // the position on the contig
-    private final char refBase;                 // the reference base
-    private final int depthOfCoverage;          // the depth of coverage at this position
-    private final int maximumMappingQual;       // the maximum mapping quality of a read at this position
-    private final DiploidGenotype genotype;     // the called genotype
-    private final double LODBestToReference;    // the LOD score of the best to the reference
-    private final double LODBestToNext;         // the LOD score of the best to the next best genotype
-    private final double likelihoods[];         // the array of all genotype likelihoods, in ordinal order
-
-    /**
-     * Create a geli text feature, given:
-     *
-     * @param contig             the contig
-     * @param position           the position on the contig
-     * @param refBase            the reference base
-     * @param depthOfCoverage    the depth of coverage at this position
-     * @param maximumMappingQual the maximum mapping quality of a read at this position
-     * @param genotype           the called genotype
-     * @param LODBestToReference the LOD score of the best to the reference
-     * @param LODBestToNext      the LOD score of the best to the next best genotype
-     * @param likelihoods        the array of all genotype likelihoods, in ordinal ordering
-     */
-    public GeliTextFeature(String contig,
-                           long position,
-                           char refBase,
-                           int depthOfCoverage,
-                           int maximumMappingQual,
-                           DiploidGenotype genotype,
-                           double LODBestToReference,
-                           double LODBestToNext,
-                           double[] likelihoods) {
-        this.contig = contig;
-        this.position = position;
-        this.refBase = refBase;
-        this.depthOfCoverage = depthOfCoverage;
-        this.maximumMappingQual = maximumMappingQual;
-        this.genotype = genotype;
-        this.LODBestToReference = LODBestToReference;
-        this.LODBestToNext = LODBestToNext;
-        this.likelihoods = likelihoods;
-    }
-
-    @Override
-    public String getContig() {
-        return this.contig;
-    }
-
-    /** Return the start position in 1-based coordinates (first base is 1) */
-    public int getStart() {
-        return (int) this.position;
-    }
-
-    /**
-     * Return the end position following 1-based fully closed conventions.  The length of a feature is
-     * end - start + 1;
-     */
-    public int getEnd() {
-        return (int) this.position;
-    }
-
-    public char getRefBase() {
-        return refBase;
-    }
-
-    public int getDepthOfCoverage() {
-        return depthOfCoverage;
-    }
-
-    public int getMaximumMappingQual() {
-        return maximumMappingQual;
-    }
-
-    public DiploidGenotype getGenotype() {
-        return genotype;
-    }
-
-    public double getLODBestToNext() {
-        return LODBestToNext;
-    }
-
-    public double getLODBestToReference() {
-        return LODBestToReference;
-    }
-
-    public double[] getLikelihoods() {
-        return likelihoods;
-    }
-
-    private static double Epsilon = 0.0001;
-    public boolean equals(Object o) {
-        if (!(o instanceof GeliTextFeature)) return false;
-        GeliTextFeature other = (GeliTextFeature)o;
-        if (!Arrays.equals(likelihoods,other.likelihoods)) return false;
-        if (!contig.equals(other.contig)) return false;
-        if (!(position == other.position)) return false;
-        if (!(refBase == other.refBase)) return false;
-        if (!(depthOfCoverage == other.depthOfCoverage)) return false;
-        if (!(maximumMappingQual == other.maximumMappingQual)) return false;
-        if (!(genotype == other.genotype)) return false;
-        if (!(Math.abs(LODBestToReference - other.LODBestToReference) < Epsilon)) return false;
-        if (!(Math.abs(LODBestToNext - other.LODBestToNext) < Epsilon)) return false;
-        return true;
-    }
-
-}