[med-svn] [Git][med-team/beagle][master] 2 commits: New upstream version 5.1-191125+dfsg
Dylan Aïssi
gitlab at salsa.debian.org
Sat Dec 14 17:58:18 GMT 2019
Dylan Aïssi pushed to branch master at Debian Med / beagle
Commits:
32b96745 by Dylan Aïssi at 2019-12-14T17:58:05Z
New upstream version 5.1-191125+dfsg
- - - - -
48f79ba9 by Dylan Aïssi at 2019-12-14T17:58:05Z
Update upstream source from tag 'upstream/5.1-191125+dfsg'
Update to upstream version '5.1-191125+dfsg'
with Debian dir fadb450493679840ab428de2b98448b709c7a3a2
- - - - -
3 changed files:
- main/Main.java
- vcf/PlinkGenMap.java
- vcf/WindowIt.java
Changes:
=====================================
main/Main.java
=====================================
@@ -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
=====================================
@@ -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
=====================================
@@ -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
View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/4d7d5a3810956f435be1cea8a9ca0260b9003170...48f79ba956e68a83da81ce02e1569537970b2550
--
View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/4d7d5a3810956f435be1cea8a9ca0260b9003170...48f79ba956e68a83da81ce02e1569537970b2550
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