[med-svn] [Git][med-team/beagle][master] 4 commits: New upstream version 5.0-190712+dfsg
Dylan Aïssi
gitlab at salsa.debian.org
Sat Jul 13 16:15:23 BST 2019
Dylan Aïssi pushed to branch master at Debian Med / beagle
Commits:
7f4a872f by Dylan Aïssi at 2019-07-13T15:09:38Z
New upstream version 5.0-190712+dfsg
- - - - -
7958ea92 by Dylan Aïssi at 2019-07-13T15:09:40Z
Update upstream source from tag 'upstream/5.0-190712+dfsg'
Update to upstream version '5.0-190712+dfsg'
with Debian dir debb749a2ca2adf6e4b5f3d10277f10bfa916c3c
- - - - -
8f1958a2 by Dylan Aïssi at 2019-07-13T15:10:40Z
Update d/changelog
- - - - -
7ad08ff5 by Dylan Aïssi at 2019-07-13T15:14:59Z
Update upstream docs
- - - - -
6 changed files:
- beagleutil/Samples.java
- debian/changelog
- debian/upstream.docs/README
- debian/upstream.docs/release_notes
- debian/upstream.docs/run.beagle.example
- main/Main.java
Changes:
=====================================
beagleutil/Samples.java
=====================================
@@ -57,8 +57,8 @@ public final class Samples {
for (int j=0; j<idIndices.length; ++j) {
int idIndex = idIndices[j];
if (idIndexToIndex[idIndex] != -1) {
- String s = "duplicate sample: " + sampleIds.id(idIndex) +
- " (ID index: " + idIndex + ")";
+ String s = "ERROR: Duplicate sample (" + sampleIds.id(idIndex) +
+ ") in target and/or reference file";
throw new IllegalArgumentException(s);
}
else {
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+beagle (5.0-190712+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream release.
+
+ -- Dylan Aïssi <daissi at debian.org> Sat, 13 Jul 2019 17:09:59 +0200
+
beagle (5.0-190703+dfsg-1) unstable; urgency=medium
* New upstream release.
=====================================
debian/upstream.docs/README
=====================================
@@ -1,10 +1,10 @@
# Author: Dylan Assi <daissi at debian.org>
-# Last-Update: 2019-07-04
+# Last-Update: 2019-07-13
# These files were downloaded from https://faculty.washington.edu/browning/beagle/
# They should be updated when upstream update them.
wget https://faculty.washington.edu/browning/beagle/beagle5_release_notes -O release_notes
wget https://faculty.washington.edu/browning/beagle/beagle_5.0_03Jul19.pdf -O beagle_5.0.pdf
- wget https://faculty.washington.edu/browning/beagle/run.beagle.03Jul19.b33.example -O run.beagle.example
- wget http://faculty.washington.edu/browning/beagle/test.03Jul19.b33.vcf.gz -O test.vcf.gz && \
+ wget https://faculty.washington.edu/browning/beagle/run.beagle.12Jul19.0df.example -O run.beagle.example
+ wget http://faculty.washington.edu/browning/beagle/test.12Jul19.0df.vcf.gz -O test.vcf.gz && \
gunzip test.vcf.gz
=====================================
debian/upstream.docs/release_notes
=====================================
@@ -59,3 +59,8 @@ Beagle 5.0 (16May19.351) release notes
Beagle 5.0 (03Jul19.b33) release notes
=============================================
* Fixed a bug when analysis includes multiple chromosomes
+
+Beagle 5.0 (12Jul19.0df) release notes
+=============================================
+* Improved an error message
+* Improved handling of inconsistent marker order in ref and gt files
=====================================
debian/upstream.docs/run.beagle.example
=====================================
@@ -1,47 +1,47 @@
#!/bin/bash
-if [ ! -f beagle.03Jul19.b33.jar ]; then
+if [ ! -f beagle.12Jul19.0df.jar ]; then
echo
- echo "Downloading beagle.03Jul19.b33.jar"
- wget http://faculty.washington.edu/browning/beagle/beagle.03Jul19.b33.jar
+ echo "Downloading beagle.12Jul19.0df.jar"
+ wget http://faculty.washington.edu/browning/beagle/beagle.12Jul19.0df.jar
fi
-if [ ! -f bref3.03Jul19.b33.jar ]; then
+if [ ! -f bref3.12Jul19.0df.jar ]; then
echo
- echo "Downloading bref3.03Jul19.b33.jar"
- wget http://faculty.washington.edu/browning/beagle/bref3.03Jul19.b33.jar
+ echo "Downloading bref3.12Jul19.0df.jar"
+ wget http://faculty.washington.edu/browning/beagle/bref3.12Jul19.0df.jar
fi
echo
-if [ ! -f test.03Jul19.b33.vcf.gz ]; then
+if [ ! -f test.12Jul19.0df.vcf.gz ]; then
echo
- echo "*** Downloading some 1000 Genomes Project data to file: test.03Jul19.b33.vcf.gz ***"
- wget http://faculty.washington.edu/browning/beagle/test.03Jul19.b33.vcf.gz
+ echo "*** Downloading some 1000 Genomes Project data to file: test.12Jul19.0df.vcf.gz ***"
+ wget http://faculty.washington.edu/browning/beagle/test.12Jul19.0df.vcf.gz
fi
echo
-echo "*** Creating test files: ref.03Jul19.b33.vcf.gz target.03Jul19.b33.vcf.gz ***"
+echo "*** Creating test files: ref.12Jul19.0df.vcf.gz target.12Jul19.0df.vcf.gz ***"
echo
-zcat test.03Jul19.b33.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.03Jul19.b33.vcf.gz
-zcat test.03Jul19.b33.vcf.gz | cut -f1-9,191-200 | gzip > target.03Jul19.b33.vcf.gz
+zcat test.12Jul19.0df.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.12Jul19.0df.vcf.gz
+zcat test.12Jul19.0df.vcf.gz | cut -f1-9,191-200 | gzip > target.12Jul19.0df.vcf.gz
echo
echo "*** Running test analysis with \"gt=\" argument ***"
echo
-java -jar beagle.03Jul19.b33.jar gt=test.03Jul19.b33.vcf.gz out=out.gt
+java -jar beagle.12Jul19.0df.jar gt=test.12Jul19.0df.vcf.gz out=out.gt
echo
echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
echo
-java -jar beagle.03Jul19.b33.jar ref=ref.03Jul19.b33.vcf.gz gt=target.03Jul19.b33.vcf.gz out=out.ref
+java -jar beagle.12Jul19.0df.jar ref=ref.12Jul19.0df.vcf.gz gt=target.12Jul19.0df.vcf.gz out=out.ref
echo
echo "*** Making \"bref3\" file ***"
echo
-java -jar bref3.03Jul19.b33.jar ref.03Jul19.b33.vcf.gz > ref.03Jul19.b33.bref3
+java -jar bref3.12Jul19.0df.jar ref.12Jul19.0df.vcf.gz > ref.12Jul19.0df.bref3
echo
echo "*** Running test analysis with \"bref3\" file ***"
echo
-java -jar beagle.03Jul19.b33.jar ref=ref.03Jul19.b33.bref3 gt=target.03Jul19.b33.vcf.gz out=out.bref3
+java -jar beagle.12Jul19.0df.jar ref=ref.12Jul19.0df.bref3 gt=target.12Jul19.0df.vcf.gz out=out.bref3
=====================================
main/Main.java
=====================================
@@ -68,8 +68,8 @@ public class Main {
* The program name and version.
*/
public static final String VERSION = "(version 5.0)";
- public static final String PROGRAM = "beagle.03Jul19.b33.jar";
- public static final String COMMAND = "java -jar beagle.03Jul19.b33.jar";
+ public static final String PROGRAM = "beagle.12Jul19.0df.jar";
+ public static final String COMMAND = "java -jar beagle.12Jul19.0df.jar";
/**
* The copyright string.
@@ -81,7 +81,7 @@ public class Main {
*/
public static final String SHORT_HELP = Main.PROGRAM + " " + VERSION
+ Const.nl + Main.COPYRIGHT
- + Const.nl + "Enter \"java -jar beagle.03Jul19.b33.jar\" to "
+ + Const.nl + "Enter \"java -jar beagle.12Jul19.0df.jar\" to "
+ "list command line argument";
private final Par par;
@@ -193,14 +193,16 @@ public class Main {
private void printOutput(CurrentData cd, GT phasedTarg) {
assert par.gt()!=null;
- int refStart = cd.prevSpliceStart();
- int refEnd = cd.nextSpliceStart();
int nThreads = par.nthreads();
if (cd.nMarkers()==cd.nTargMarkers() || par.impute() == false) {
- windowWriter.print(phasedTarg, refStart, refEnd, nThreads);
+ int targStart = cd.prevTargetSpliceStart();
+ int targEnd = cd.nextTargetSpliceStart();
+ windowWriter.print(phasedTarg, targStart, targEnd, nThreads);
}
else {
long t0 = System.nanoTime();
+ int refStart = cd.prevSpliceStart();
+ int refEnd = cd.nextSpliceStart();
ImpData impData = new ImpData(par, cd, phasedTarg, genMap);
AtomicReferenceArray<StateProbs> stateProbs = ImpLS.stateProbs(impData);
windowWriter.print(impData, stateProbs, refStart, refEnd);
View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/7fb6efca61e183376354eaa49315298ce1d37e91...7ad08ff53ee6dfd20f9a9d93cfc91774c664f9e0
--
View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/7fb6efca61e183376354eaa49315298ce1d37e91...7ad08ff53ee6dfd20f9a9d93cfc91774c664f9e0
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