New upstream version 5.1-191125+dfsg (32b96745) · Commits · Debian Med / beagle

main/Main.java

+3 −3

Original line number	Diff line number	Diff line
		@@ -65,8 +65,8 @@ public class Main {
		* The program name and version.
		*/
		public static final String VERSION = "(version 5.1)";
		public static final String PROGRAM = "beagle.20Nov19.573.jar";
		public static final String COMMAND = "java -jar beagle.20Nov19.573.jar";
		public static final String PROGRAM = "beagle.25Nov19.28d.jar";
		public static final String COMMAND = "java -jar beagle.25Nov19.28d.jar";

		/**
		* The copyright string.
		@@ -78,7 +78,7 @@ public class Main {
		*/
		public static final String SHORT_HELP = Main.PROGRAM + " " + VERSION
		+ Const.nl + Main.COPYRIGHT
		+ Const.nl + "Enter \"java -jar beagle.20Nov19.573.jar\" to "
		+ Const.nl + "Enter \"java -jar beagle.25Nov19.28d.jar\" to "
		+ "list command line argument";

		private final Par par;

vcf/PlinkGenMap.java

+40 −24

Original line number	Diff line number	Diff line
		@@ -307,11 +307,11 @@ public final class PlinkGenMap implements GeneticMap {

		@Override
		public double genPos(int chrom, int basePosition) {
		double minEndCm = 5.0;
		checkChromIndex(chrom);
		int mapSize = basePos[chrom].length;
		assert mapSize>=2;
		assert genPos[chrom].length==mapSize;
		double minEndCmDist = 5.0;
		int mapSizeM1 = basePos[chrom].length - 1;
		assert mapSizeM1>0;
		assert genPos[chrom].length==basePos[chrom].length;
		int index = Arrays.binarySearch(basePos[chrom], basePosition);
		if (index>=0) {
		return genPos[chrom][index];
		@@ -319,23 +319,23 @@ public final class PlinkGenMap implements GeneticMap {
		int insPt = -index-1;
		int aIndex = insPt - 1;
		int bIndex = insPt;
		if (insPt==mapSize) {
		insPt = Arrays.binarySearch(genPos[chrom], genPos[chrom][mapSize-1] - minEndCm);
		if (aIndex==mapSizeM1) {
		insPt = Arrays.binarySearch(genPos[chrom], genPos[chrom][mapSizeM1] - minEndCmDist);
		if (insPt<0) {
		insPt = -insPt - 2;
		}
		assert insPt<(mapSize-1);
		assert insPt<mapSizeM1;
		aIndex = Math.max(insPt, 0);
		bIndex = mapSize-1;
		bIndex = mapSizeM1;
		}
		else if (insPt==0) {
		insPt = Arrays.binarySearch(genPos[chrom], genPos[chrom][0] + minEndCm);
		else if (bIndex==0) {
		insPt = Arrays.binarySearch(genPos[chrom], genPos[chrom][0] + minEndCmDist);
		if (insPt<0) {
		insPt = -insPt - 1;
		}
		assert insPt>0;
		aIndex = 0;
		bIndex = Math.min(insPt, mapSize-1);
		bIndex = Math.min(insPt, mapSizeM1);
		}
		int x = basePosition;
		int a = basePos[chrom][aIndex];
		@@ -349,30 +349,46 @@ public final class PlinkGenMap implements GeneticMap {
		@Override
		public int basePos(int chrom, double geneticPosition) {
		checkChromIndex(chrom);
		assert basePos[chrom].length>=2;
		int minEndBasepairDist = 5_000_000;
		int mapSizeM1 = genPos[chrom].length - 1;
		assert mapSizeM1>0;
		assert basePos[chrom].length==genPos[chrom].length;
		int index = Arrays.binarySearch(genPos[chrom], geneticPosition);
		if (index>=0) {
		return basePos[chrom][index];
		} else {
		int insPt = -index-1;
		if (insPt==genPos[chrom].length) {
		--insPt;
		while (genPos[chrom][insPt]==genPos[chrom][insPt-1]) {
		--insPt;
		int aIndex = insPt - 1;
		int bIndex = insPt;
		if (aIndex==mapSizeM1) {
		insPt = Arrays.binarySearch(basePos[chrom], basePos[chrom][mapSizeM1] - minEndBasepairDist);
		if (insPt<0) {
		insPt = -insPt - 2;
		}
		assert insPt<mapSizeM1;
		aIndex = Math.max(insPt, 0);
		bIndex = mapSizeM1;
		while (genPos[chrom][aIndex]==genPos[chrom][bIndex] && aIndex>0) {
		--aIndex;
		}
		}
		else if (insPt==0) {
		++insPt;
		while (genPos[chrom][insPt]==genPos[chrom][insPt-1]) {
		++insPt;
		else if (bIndex==0) {
		insPt = Arrays.binarySearch(basePos[chrom], basePos[chrom][0] + minEndBasepairDist);
		if (insPt<0) {
		insPt = -insPt - 1;
		}
		assert insPt>0;
		aIndex = 0;
		bIndex = Math.min(insPt, mapSizeM1);
		while (genPos[chrom][aIndex]==genPos[chrom][bIndex] && bIndex<mapSizeM1) {
		++bIndex;
		}
		}
		double x = geneticPosition;
		double a = genPos[chrom][insPt-1];
		double b = genPos[chrom][insPt];
		int fa = basePos[chrom][insPt-1];
		int fb = basePos[chrom][insPt];
		double a = genPos[chrom][aIndex];
		double b = genPos[chrom][bIndex];
		int fa = basePos[chrom][aIndex];
		int fb = basePos[chrom][bIndex];
		double interp = ((x-a)/(b-a)) * (fb-fa);
		if (interp>=Integer.MAX_VALUE) {
		String s = "Base position exceeds Integer.MAX_VALUE"

vcf/WindowIt.java

+1 −1

Original line number	Diff line number	Diff line
		@@ -260,7 +260,7 @@ public class WindowIt<E extends GTRec> implements SampleFileIt<Window<E>> {
		}
		int endPos = genMap.basePos(chromIndex, endCm);
		int overlapEnd = nextList.size();
		nextList.add(next); // ensure at least on record is added
		nextList.add(next); // ensure at least one record is added
		next = it.hasNext() ? it.next() : null;
		while (next!=null
		&& next.marker().chromIndex()==chromIndex