Commit 984ed8b0 authored by Dylan Aïssi's avatar Dylan Aïssi
Browse files

New upstream version 5.0-180928+dfsg

parent 169b5c18

blbutil/ByteArray.java

deleted100644 → 0
+0 −128
Original line number Diff line number Diff line 
/*

 * Copyright (C) 2014-2016 Brian L. Browning

 *

 * This file is part of Beagle

 *

 * Beagle is free software: you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation, either version 3 of the License, or

 * (at your option) any later version.

 *

 * Beagle is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU General Public License for more details.

 *

 * You should have received a copy of the GNU General Public License

 * along with this program.  If not, see <http://www.gnu.org/licenses/>.

 */

package blbutil;



/**

 * <p>Class {@code ByteArray} represents an immutable array of integer

 * values between -128 and 127 that is stored as a {@code byte[]} array.

 * </p>

 * Instances of {@code ByteArray} are immutable.

 *

 * @author Brian L. Browning {@code <browning@uw.edu>}

 */

public final class ByteArray implements IntArray {



    private final byte[] ba;



    /**

     * Constructs a new {@code ByteArray} instance from

     * the specified data.

     * @param ba an array of integer values between -128 and 127 inclusive

     * @throws NullPointerException if {@code ba == null}

     */

    public ByteArray(byte[] ba) {

        this.ba = ba.clone();

    }



    /**

     * Constructs a new {@code ByteArray} instance from the specified data.

     * @param ia an array of integer values between -128 and 127 inclusive

     * @throws IllegalArgumentException if

     * {@code (ia[j] < -128 || ia[j] > 127)} for any index {@code j}

     * satisfying  {@code (j >= 0 && j < ia.length)}

     * @throws NullPointerException if {@code ia == null}

     */

    public ByteArray(int[] ia) {

        this(ia, 0, ia.length);

    }



    /**

     * Constructs a new {@code ByteArray} instance from the specified data.

     * @param il an list of integer values between -128 and 127 inclusive

     * @throws IllegalArgumentException if

     * {@code (il.get(j) < -128 || il.get(j) > 127)} for any index {@code j}

     * satisfying  {@code (j >= 0 && j < il.size())}

     * @throws NullPointerException if {@code il == null}

     */

    public ByteArray(IntList il) {

        this(il, 0, il.size());

    }



    /**

     * Constructs a new {@code ByteArray} instance from the

     * specified data.

     * @param ia an array of integer values between -128 and 127 inclusive

     * @param from the first element to be included (inclusive)

     * @param to the last element to be included (exclusive)

     * @throws IllegalArgumentException if

     * {@code (ia[j] < -128 || ia[j] > 127)} for any index {@code j}

     * satisfying  {@code (j >= from && j < to)}

     * @throws IndexOutOfBoundsException if {@code from < 0 || to > ia.length}

     * @throws NegativeArraySizeException if {@code to > from}

     * @throws NullPointerException if {@code ia == null}

     */

    public ByteArray(int[] ia, int from, int to) {

        this.ba = new byte[to - from];

        for (int j=from; j<to; ++j) {

            if (ia[j] < -128 || ia[j] > 127) {

                throw new IllegalArgumentException(String.valueOf(ia[j]));

            }

            ba[j - from] = (byte) ia[j];

        }

    }



    /**

     * Constructs a new {@code ByteArray} instance from the

     * specified data.

     * @param il an list of integer values between -128 and 127 inclusive

     * @param from the first element to be included (inclusive)

     * @param to the last element to be included (exclusive)

     * @throws IllegalArgumentException if

     * {@code (il.get(j) < -128 || il.get(j) > 127)} for any index {@code j}

     * satisfying  {@code (j >= from && j < to)}

     * @throws IndexOutOfBoundsException if {@code from < 0 || to > il.length}

     * @throws NegativeArraySizeException if {@code to > from}

     * @throws NullPointerException if {@code il == null}

     */

    public ByteArray(IntList il, int from, int to) {

        this.ba = new byte[to - from];

        for (int j=from; j<to; ++j) {

            int value = il.get(j);

            if (value < -128 || value > 127) {

                throw new IllegalArgumentException(String.valueOf(value));

            }

            ba[j - from] = (byte) value;

        }

    }



    @Override

    public int size() {

        return ba.length;

    }



    @Override

    public int get(int index) {

        return ba[index];

    }



    @Override

    public String toString() {

        return this.asString();

    }

}

blbutil/Utilities.java

+14 −0
Original line number Diff line number Diff line
@@ -99,6 +99,20 @@ public class Utilities { 
        return sdf.format(now);

    }



    /**

     * Returns the current minutes and seconds as a string.  The

     * exact details of the string representation

     * are unspecified and subject to change.

     *

     * @return the current local time as a string.

     */

    public static String minutesAndSeconds() {

        Date now = new Date();

        SimpleDateFormat sdf =

                new SimpleDateFormat("mm:ss");

        return sdf.format(now);

    }



    /**

     * <p>Returns a set of identifiers found in a text file that has

     * one identifier per line.  The empty set is returned if

bref/AsIsBref3Writer.java

+39 −12
Original line number Diff line number Diff line
@@ -21,8 +21,8 @@ package bref; 
import beagleutil.ChromIds;

import beagleutil.Samples;

import blbutil.FileUtil;

import blbutil.IntArray;

import blbutil.IntList;

import ints.IntArray;

import ints.IntList;

import blbutil.Utilities;

import java.io.ByteArrayOutputStream;

import java.io.DataOutputStream;
@@ -54,6 +54,31 @@ import vcf.RefGTRec; 
 */

public class AsIsBref3Writer implements BrefWriter {



    /**

     * The end of file code for a bref file.

     */

    public static final int END_OF_DATA = 0;



    /**

     * The integer denoting denoting the end of the index in a bref file

     */

    public static final long END_OF_INDEX = -999_999_999_999_999L;



    /**

     * The initial integer in a bref version 3 file.

     */

    public static final int MAGIC_NUMBER_V3 = 2055763188;



    /**

     * The byte value denoting a sequence coded record

     */

    public static final byte SEQ_CODED = 0;



    /**

     * The byte value denoting an allele coded record

     */

    public static final byte ALLELE_CODED = 1;



    private final String WRITE_ERR = "Error writing file";

    private final String CONTIGUITY_ERR = "Error: chromosomes not contiguous";
@@ -62,7 +87,6 @@ public class AsIsBref3Writer implements BrefWriter { 
    private final Comparator<String[]> ALLELES_COMP = allelesComparator();



    public final int MAX_SAMPLES = (1 << 29) - 1;

    public final int MAX_BLOCK_BYTES = Integer.MAX_VALUE;



    private int lastChromIndex = -1;

    private IntArray hap2Seq = null;
@@ -145,10 +169,10 @@ public class AsIsBref3Writer implements BrefWriter { 
        }

        if (rec.isAlleleCoded()==false) {

            if (hap2Seq==null) {

                hap2Seq = rec.hapToSeq();

                hap2Seq = rec.map(0);

            }

            else if (rec.hapToSeq()!=hap2Seq) {

                hap2Seq = rec.hapToSeq();

            else if (rec.map(0)!=hap2Seq) {

                hap2Seq = rec.map(0);

                startNewBlock = true;

            }

        }
@@ -214,10 +238,12 @@ public class AsIsBref3Writer implements BrefWriter { 
            }

        }

        else {

            brefOut.writeChar(rec.seqToAllele().size());

            IntArray hap2seq = rec.hapToSeq();

            for (int j=0, n=hap2seq.size(); j<n; ++j) {

                brefOut.writeChar(hap2seq.get(j));

            assert rec.nMaps()==2;

            IntArray hapToSeq = rec.map(0);

            IntArray seqToAllele = rec.map(1);

            brefOut.writeChar(seqToAllele.size());

            for (int j=0, n=hapToSeq.size(); j<n; ++j) {

                brefOut.writeChar(hapToSeq.get(j));

            }

        }

        bytesWritten += (nHaps + 1)*Character.BYTES;
@@ -227,7 +253,8 @@ public class AsIsBref3Writer implements BrefWriter { 
        if (rec.nAlleles() >= 256) {

            Utilities.exit("ERROR: more than 256 alleles: " + rec.marker());

        }

        IntArray seq2Allele = rec.seqToAllele();

        assert rec.nMaps()==2;

        IntArray seq2Allele = rec.map(1);

        writeMarker(rec.marker());

        brefOut.writeByte(SEQ_CODED);

        for (int j=0, n=seq2Allele.size(); j<n; ++j) {
@@ -367,7 +394,7 @@ public class AsIsBref3Writer implements BrefWriter { 
    }



    private DataOutputStream dataOutputStream(File file) {

        OutputStream dos = null;

        OutputStream dos;

        if (file==null) {

            dos = new DataOutputStream(System.out);

        }

bref/Bref3It.java

+1 −1
Original line number Diff line number Diff line
@@ -55,7 +55,7 @@ public final class Bref3It implements SampleFileIt<RefGTRec> { 


    /**

     * Constructs a new {@code Bref3It} instance.

     * @param brefFile a bref version 3 file or {@null} if the

     * @param brefFile a bref version 3 file or {@code null} if the

     * bref version 3 file is to be read from standard input

     *

     * @throws IllegalArgumentException if a format error is detected in a

bref/Bref3Reader.java

+4 −4
Original line number Diff line number Diff line
@@ -20,11 +20,11 @@ package bref; 


import beagleutil.ChromIds;

import beagleutil.Samples;

import blbutil.CharArray;

import ints.CharArray;

import blbutil.Const;

import blbutil.Filter;

import blbutil.IntArray;

import blbutil.UnsignedByteArray;

import ints.IntArray;

import ints.UnsignedByteArray;

import blbutil.Utilities;

import java.io.DataInput;

import java.io.IOException;
@@ -185,7 +185,7 @@ public final class Bref3Reader { 


    private static void readAndCheckMagicNumber(DataInput di) throws IOException {

        int magicNumber=di.readInt();

        if (magicNumber!=BrefWriter.MAGIC_NUMBER_V3) {

        if (magicNumber!=AsIsBref3Writer.MAGIC_NUMBER_V3) {

            String s = "ERROR: Unrecognized input file.  Was input file created "

                    + Const.nl + "with a different version of the bref program?";

            Utilities.exit(s);