New upstream version 5.1-190824+dfsg (9ea91de8) · Commits · Debian Med / beagle

beagleutil/ChromInterval.java

+3 −3

Original line number	Diff line number	Diff line
		@@ -205,7 +205,7 @@ public final class ChromInterval implements IntInterval,
		* @return the last genome coordinate in this chromosome interval.
		*/
		@Override
		public int end() {
		public int inclEnd() {
		return end;
		}

		@@ -332,7 +332,7 @@ public final class ChromInterval implements IntInterval,
		return false;
		}
		else {
		return (a.start() <= b.end()) && (b.start() <= a.end());
		return (a.start() <= b.inclEnd()) && (b.start() <= a.inclEnd());
		}
		}

		@@ -350,7 +350,7 @@ public final class ChromInterval implements IntInterval,
		throw new IllegalArgumentException(s);
		}
		int start = Math.min(a.start(), b.start());
		int end = Math.max(a.end(), b.end());
		int end = Math.max(a.inclEnd(), b.inclEnd());
		return new ChromInterval(a.chrom(), start, end);
		}
		}

beagleutil/IntInterval.java

+7 −7

Original line number	Diff line number	Diff line
		@@ -40,13 +40,13 @@ public interface IntInterval {
		* Returns the end of the interval (inclusive).
		* @return the end of the interval (inclusive).
		*/
		public int end();
		public int inclEnd();

		/**
		* Returns a {@code Comparator<IntInterval>} which orders
		* {@code IntInterval} objects in order of increasing {@code this.start()}
		* value and orders {@code IntInterval} objects with the same
		* {@code this.start()} value in order of increasing {@code this.end()}
		* {@code this.start()} value in order of increasing {@code this.inclEnd()}
		* value.
		* @return a {@code Comparator<IntInterval>} object
		*/
		@@ -55,8 +55,8 @@ public interface IntInterval {
		if (t1.start() != t2.start()) {
		return (t1.start() < t2.start()) ? -1 : 1;
		}
		else if (t1.end() != t2.end()) {
		return (t1.end() < t2.end()) ? -1 : 1;
		else if (t1.inclEnd() != t2.inclEnd()) {
		return (t1.inclEnd() < t2.inclEnd()) ? -1 : 1;
		}
		return 0;
		} ;
		@@ -66,7 +66,7 @@ public interface IntInterval {
		* Returns a {@code Comparator<IntInterval>} which orders
		* {@code IntInterval} objects in order of increasing {@code this.start()}
		* value and orders {@code IntInterval} objects with the same
		* {@code this.start()} value in order of decreasing {@code this.end()}
		* {@code this.start()} value in order of decreasing {@code this.inclEnd()}
		* value.
		* @return a {@code Comparator<IntInterval>} object
		*/
		@@ -75,8 +75,8 @@ public interface IntInterval {
		if (t1.start() != t2.start()) {
		return (t1.start() < t2.start()) ? -1 : 1;
		}
		else if (t1.end() != t2.end()) {
		return (t1.end() > t2.end()) ? -1 : 1;
		else if (t1.inclEnd() != t2.inclEnd()) {
		return (t1.inclEnd() > t2.inclEnd()) ? -1 : 1;
		}
		return 0;
		} ;

beagleutil/PbwtUpdater.java

0 → 100644

+190 −0

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 beagleutil;

		import ints.IntArray;
		import ints.IntList;
		import java.util.Arrays;
		import java.util.stream.IntStream;

		/**
		* <p>Class {@code PbwtUpdater} updates prefix and divergence arrays using
		* the positional Burrows-Wheeler transform (PBWT).</p>
		*
		* <p>Instances of {@code PbwtUpdater} are not thread-safe.</p>
		*
		* <p>Reference: Durbin, Richard (2014) Efficient haplotype matching and storage
		* using the positional Burrows-Wheeler transform (PBWT).
		* Bioinformatics 30(9):166-1272. doi: 10.1093/bioinformatics/btu014</p>
		*
		* @author Brian L. Browning {@code <browning@uw.edu>}
		*/
		public class PbwtUpdater {

		private final int nHaps;

		private IntList[] a; // next prefix array data
		private IntList[] d; // next div array data
		private int[] p;

		/**
		* Constructs a new {@code PbwtUpdater} instance for the specified data.
		* @param nHaps the number of haplotypes at each position
		* @throws NegativeArraySizeException if {@code nHaps < 0}
		*/
		public PbwtUpdater(int nHaps) {
		int initSize = 4;
		this.nHaps = nHaps;
		this.p = new int[initSize];
		this.a = IntStream.range(0, initSize)
		.mapToObj(i -> new IntList())
		.toArray(IntList[]::new);
		this.d = IntStream.range(0, initSize)
		.mapToObj(i -> new IntList())
		.toArray(IntList[]::new);
		}

		/**
		* Returns the number of haplotypes.
		* @return the number of haplotypes
		*/
		public int nHaps() {
		return nHaps;
		}

		/**
		* Update the specified prefix and divergence arrays using the forward
		* Positional Burrows-Wheeler Transform. The contract for this method is
		* undefined if the specified {@code prefix} array is not a permutation of
		* {@code 0, 1, 2, ..., (nHaps - 1)}, or if the elements of the
		* specified {@code div} arrays are not all less than or equal to
		* the specified {@code marker}.
		*
		* @param rec the haplotype alleles
		* @param nAlleles the number of alleles
		* @param marker the marker index for the specified haplotype alleles
		* @param prefix the prefix array
		* @param div the divergence array
		*
		* @throws IllegalArgumentException if {@code nAlleles < 1}
		* @throws IndexOutOfBoundsException if
		* {@code (rec.get[j] < 0 \|\| rec.get(j) >= nAlleles)}
		* for any {@code j} satisfying {@code (0 <= j && j < this.nHaps())}
		* @throws IndexOutOfBoundsException if {@code prefix.length >= this.nHaps()}
		* @throws IndexOutOfBoundsException if {@code div.length >= this.nHaps()}
		* @throws NullPointerException if
		* {@code rec == null \|\| prefix == null \|\| div == null}
		*/
		public void fwdUpdate(IntArray rec, int nAlleles, int marker, int[] prefix,
		int[] div) {
		initializeArrays(nAlleles, marker+1);
		for (int i=0; i<nHaps; ++i) {
		int allele = rec.get(prefix[i]);
		if (allele>=nAlleles) {
		throw new IndexOutOfBoundsException(String.valueOf(nAlleles));
		}
		for (int j=0; j<nAlleles; ++j) {
		if (div[i]>p[j]) {
		p[j] = div[i];
		}
		}
		a[allele].add(prefix[i]);
		d[allele].add(p[allele]);
		p[allele] = Integer.MIN_VALUE;
		}
		updatePrefixAndDiv(nAlleles, prefix, div);
		}

		/**
		* Update the specified prefix and divergence arrays using the backward
		* Positional Burrows-Wheeler Transform. The contract for this method is
		* undefined if the specified {@code prefix} array is not a permutation of
		* {@code 0, 1, 2, ..., (nHaps - 1)}, or if the elements of the
		* specified {@code div} arrays are not all greater than or equal to
		* the specified {@code marker}.
		*
		* @param rec the haplotype alleles
		* @param nAlleles the number of alleles
		* @param marker the marker index for the specified haplotype alleles
		* @param prefix the prefix array
		* @param div the divergence array
		*
		* @throws IllegalArgumentException if {@code nAlleles < 1}
		* @throws IndexOutOfBoundsException if
		* {@code (rec.get[j] < 0 \|\| rec.get(j) >= nAlleles)}
		* for any {@code j} satisfying {@code (0 <= j && j < this.nHaps())}
		* @throws IndexOutOfBoundsException if {@code prefix.length >= this.nHaps()}
		* @throws IndexOutOfBoundsException if {@code div.length >= this.nHaps()}
		* @throws NullPointerException if
		* {@code rec == null \|\| prefix == null \|\| div == null}
		*/
		public void bwdUpdate(IntArray rec, int nAlleles, int marker, int[] prefix,
		int[] div) {
		initializeArrays(nAlleles, marker-1);
		for (int i=0; i<nHaps; ++i) {
		int allele = rec.get(prefix[i]);
		if (allele>=nAlleles) {
		throw new IndexOutOfBoundsException(String.valueOf(nAlleles));
		}
		for (int j=0; j<nAlleles; ++j) {
		if (div[i]<p[j]) {
		p[j] = div[i];
		}
		}
		a[allele].add(prefix[i]);
		d[allele].add(p[allele]);
		p[allele] = Integer.MAX_VALUE;
		}
		updatePrefixAndDiv(nAlleles, prefix, div);
		}

		private void updatePrefixAndDiv(int nAlleles, int[] prefix, int[] div) {
		int start = 0;
		for (int al=0; al<nAlleles; ++al) {
		int size = a[al].size();
		System.arraycopy(a[al].toArray(), 0, prefix, start, size);
		System.arraycopy(d[al].toArray(), 0, div, start, size);
		start += size;
		a[al].clear();
		d[al].clear();
		}
		assert start == nHaps;
		}

		private void initializeArrays(int nAlleles, int initPValue) {
		if (nAlleles<1) {
		throw new IllegalArgumentException(String.valueOf(nAlleles));
		}
		ensureArrayCapacity(nAlleles);
		Arrays.fill(p, 0, nAlleles, initPValue);
		}

		private void ensureArrayCapacity(int nAlleles) {
		if (nAlleles>a.length) {
		int oldLength = a.length;
		p = Arrays.copyOf(p, nAlleles);
		a = Arrays.copyOf(a, nAlleles);
		d = Arrays.copyOf(d, nAlleles);
		for (int j = oldLength; j<a.length; ++j) {
		a[j] = new IntList();
		d[j] = new IntList();
		}
		}
		}
		}

haplotype/HapPair.java→blbutil/DoubleArray.java

+92 −0

Original line number	Diff line number	Diff line
		@@ -16,85 +16,77 @@
		* 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 haplotype;
		package blbutil;

		import beagleutil.Samples;
		import java.util.Comparator;
		import vcf.Marker;
		import vcf.Markers;
		import java.util.Arrays;

		/**
		* <p>Interface {@code HapPair} represents a pair of haplotypes for a sample.
		* The pair of haplotypes are guaranteed to have non-missing alleles at each
		* marker.
		* </p>
		* All instances of {@code HapPair} are required to be immutable.
		* Class {@code DoubleArray} represents an immutable list of double floating
		* point values.
		*
		* @author Brian L. Browning {@code <browning@uw.edu>}
		*/
		public interface HapPair {
		public class DoubleArray {

		/**
		* Returns the first allele for the specified marker.
		* @param marker a marker index
		* @return the first allele for the specified marker
		* @throws IndexOutOfBoundsException if
		* {@code marker < 0 \|\| marker >= this.nMarkers()}
		*/
		int allele1(int marker);
		private final double[] values;

		/**
		* Returns the second allele for the specified marker.
		* @param marker a marker index
		* @return the second allele for the specified marker
		* @throws IndexOutOfBoundsException if
		* {@code marker < 0 \|\| marker >= this.nMarkers()}
		* Constructs an {@code DoubleArray} object with the specified
		* values.
		* @param values the list of floating point values
		* @throws NullPointerException if {@code values == null}
		*/
		int allele2(int marker);
		public DoubleArray(double[] values) {
		this.values = values.clone();
		}

		/**
		* Returns the markers.
		* @return the markers
		* Returns the double at the specified position in this list.
		* @param index the index of the returned double
		* @return the double at the specified position in this list
		* @throws IndexOutOfBoundsException if
		* {@code index < 0 \|\| index >= this.size()}
		*/
		Markers markers();
		public double get(int index) {
		return values[index];
		}

		/**
		* Returns the specified marker.
		* @param marker a marker index
		* @return the specified marker
		* @throws IndexOutOfBoundsException if
		* {@code marker < 0 \|\| marker >= this.nMarkers()}
		* Returns the number of elements in this list.
		* @return the number of elements in this list
		*/
		Marker marker(int marker);
		public int size() {
		return values.length;
		}

		/**
		* Returns the number of markers.
		* @return the number of markers
		* Returns {@code true} if this list has no elements, and returns
		* {@code false} otherwise.
		* @return {@code true} if this list has no elements, and returns
		* {@code false} otherwise
		*/
		int nMarkers();
		public boolean isEmpty() {
		return values.length==0;
		}

		/**
		* Returns the sample identifier index.
		* @return the sample identifier index
		* Returns an integer array containing the sequence of elements in this
		* list.
		* @return an integer array containing the sequence of elements in this
		* list
		*/
		int idIndex();
		public double[] toArray() {
		return values.clone();
		}

		/**
		* Returns a {@code Comparator<HapPairInterface>}
		* whose {@code compare(hp1, hp2)} method returns -1, 0, or 1
		* depending on whether {@code samples.index(hp1.idIndex())} is
		* less than, equal, or greater than
		* {@code samples.index(hp2.idIndex())}.
		* @param samples the list of samples used to compare {@code HapsPair}
		* objects
		* @return a {@code Comparator<HapPairInterface>}
		* whose {@code compare(hp1, hp2)} method compares two
		* haplotype pairs for order
		* @throws NullPointerException if {@code samples == null}
		* Returns a string representation of this list that is
		* obtained by calling {@code java.util.Arrays.toString(this.toArray())}.
		*
		* @return a string representation of this list
		*/
		static Comparator<HapPair> comparator(final Samples samples) {
		return (hp1, hp2) -> Integer.compare(
		samples.index(hp1.idIndex()),
		samples.index(hp2.idIndex()));
		@Override
		public String toString() {
		return Arrays.toString(values);
		}
		}

blbutil/FloatArray.java

+13 −0

Original line number	Diff line number	Diff line
		@@ -40,6 +40,19 @@ public class FloatArray {
		this.values = values.clone();
		}

		/**
		* Constructs an {@code FloatArray} object with the specified
		* values.
		* @param values the list of floating point values
		* @throws NullPointerException if {@code values == null}
		*/
		public FloatArray(double[] values) {
		this.values = new float[values.length];
		for (int j=0; j<values.length; ++j) {
		this.values[j] = (float) values[j];
		}
		}

		/**
		* Returns the float at the specified position in this list.
		* @param index the index of the returned float