[med-svn] [Git][med-team/beagle][master] 7 commits: Rename bref.jar to bref3.jar according to upstream changes
Dylan Aïssi
gitlab at salsa.debian.org
Sun Sep 16 13:23:34 BST 2018
Dylan Aïssi pushed to branch master at Debian Med / beagle
Commits:
56aefc00 by Dylan Aïssi at 2018-09-16T08:55:32Z
Rename bref.jar to bref3.jar according to upstream changes
- - - - -
f3634611 by Dylan Aïssi at 2018-09-16T09:07:32Z
Update upstream.docs
- - - - -
932c3951 by Dylan Aïssi at 2018-09-16T11:38:06Z
Fix autopkgtest
- - - - -
b1ae1734 by Dylan Aïssi at 2018-09-16T11:55:39Z
Add lintian override for embedded-javascript-library
- - - - -
169b5c18 by Dylan Aïssi at 2018-09-16T12:01:59Z
New upstream version 5.0-180915+dfsg
- - - - -
131a6fe5 by Dylan Aïssi at 2018-09-16T12:02:00Z
Merge tag 'upstream/5.0-180915+dfsg'
Upstream version 5.0-180915+dfsg
- - - - -
6bef376f by Dylan Aïssi at 2018-09-16T12:12:26Z
Upload to unstable
- - - - -
20 changed files:
- debian/beagle-doc.doc-base
- debian/beagle-doc.install
- + debian/beagle-doc.lintian-overrides
- debian/beagle.install
- debian/beagle.links
- debian/beagle.manpages
- debian/bref.1 → debian/bref3.1
- debian/changelog
- debian/rules
- debian/source/include-binaries
- debian/tests/run-sample-analysis
- debian/upstream.docs/README
- − debian/upstream.docs/beagle_4.1.pdf
- + debian/upstream.docs/beagle_5.0.pdf
- debian/upstream.docs/release_notes
- debian/upstream.docs/run.beagle.example
- imp/ImputedRecBuilder.java
- imp/ImputedVcfWriter.java
- main/Main.java
- main/MainHelper.java
Changes:
=====================================
debian/beagle-doc.doc-base
=====================================
@@ -1,9 +1,9 @@
Document: beagle
-Title: Beagle 4.1
+Title: Beagle
Section: Science/Biology
Format: PDF
-Files: /usr/share/doc/beagle/beagle_4.1.pdf.gz
+Files: /usr/share/doc/beagle/beagle_5.0.pdf.gz
Format: HTML
Index: /usr/share/doc/beagle/api/index.html
=====================================
debian/beagle-doc.install
=====================================
@@ -1,5 +1,5 @@
debian/tests/run-sample-analysis /usr/share/doc/beagle/examples/
debian/upstream.docs/run.beagle.example /usr/share/doc/beagle/examples/
debian/upstream.docs/test.vcf /usr/share/doc/beagle/examples/
-debian/upstream.docs/beagle_4.1.pdf /usr/share/doc/beagle/
+debian/upstream.docs/beagle_5.0.pdf /usr/share/doc/beagle/
debian/_jh_build.javadoc/api /usr/share/doc/beagle
=====================================
debian/beagle-doc.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# jQuery from libjs-jquery is not compatible
+beagle-doc: embedded-javascript-library * please use libjs-jquery
+beagle-doc: embedded-javascript-library * please use libjs-jquery-ui
=====================================
debian/beagle.install
=====================================
@@ -1,2 +1,2 @@
beagle.jar /usr/share/beagle/
-bref.jar /usr/share/beagle/
\ No newline at end of file
+bref3.jar /usr/share/beagle/
\ No newline at end of file
=====================================
debian/beagle.links
=====================================
@@ -1,2 +1,2 @@
/usr/share/beagle/beagle.jar usr/bin/beagle
-/usr/share/beagle/bref.jar usr/bin/bref
\ No newline at end of file
+/usr/share/beagle/bref3.jar usr/bin/bref3
\ No newline at end of file
=====================================
debian/beagle.manpages
=====================================
@@ -1,2 +1,2 @@
debian/beagle.1
-debian/bref.1
+debian/bref3.1
=====================================
debian/bref.1 → debian/bref3.1
=====================================
=====================================
debian/changelog
=====================================
@@ -1,11 +1,12 @@
-beagle (5.0-180703+dfsg-1) UNRELEASED; urgency=medium
+beagle (5.0-180915+dfsg-1) unstable; urgency=medium
* New upstream release.
* During build copy *.java files in SRC/ to avoid problem with jh_build.
* Update VCS to salsa.
* Standards-Version: 4.2.1 (no changes needed).
+ * Rename bref.jar to bref3.jar according to upstream changes.
- -- Dylan Aïssi <bob.dybian at gmail.com> Sun, 09 Sep 2018 14:22:44 +0200
+ -- Dylan Aïssi <bob.dybian at gmail.com> Sun, 16 Sep 2018 14:02:32 +0200
beagle (4.1~180127+dfsg-1) unstable; urgency=medium
=====================================
debian/rules
=====================================
@@ -10,7 +10,7 @@ override_jh_build:
mkdir SRC/
cp -t SRC/ -r beagleutil blbutil bref haplotype imp main math phase sample vcf
jh_build --javacopts="-source 1.8" --javadoc-opts="-source 1.8" --main="main.Main" beagle.jar SRC/
- jh_build --javacopts="-source 1.8" --javadoc-opts="-source 1.8" --main="bref.Bref3" bref.jar SRC/
+ jh_build --javacopts="-source 1.8" --javadoc-opts="-source 1.8" --main="bref.Bref3" bref3.jar SRC/
override_dh_installchangelogs:
dh_installchangelogs debian/upstream.docs/release_notes
=====================================
debian/source/include-binaries
=====================================
@@ -1,2 +1,3 @@
debian/upstream.docs/beagle_4.1_09Feb16.docx
debian/upstream.docs/beagle_4.1.pdf
+debian/upstream.docs/beagle_5.0.pdf
=====================================
debian/tests/run-sample-analysis
=====================================
@@ -2,7 +2,7 @@
# http://dep.debian.net/deps/dep8/
# Autopkgtest: Test if beagle run analysis correctly
# Author: Dylan Aïssi <bob.dybian at gmail.com>
-# Last-Update: 2016-06-17
+# Last-Update: 2018-09-16
pkg=beagle
if [ "$ADTTMP" = "" ] ; then
@@ -16,18 +16,15 @@ BEAGLE_TEST='java -jar /usr/share/beagle/beagle.jar'
# Generate necessary files
zcat test.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.vcf.gz
zcat test.vcf.gz | cut -f1-9,191-200 | gzip > target.vcf.gz
-java -jar /usr/share/beagle/bref.jar ref.vcf.gz
+java -jar /usr/share/beagle/bref3.jar ref.vcf.gz > ref.bref3
# Beagle with gt argument
$BEAGLE_TEST gt=test.vcf.gz out=out.gt
-# Beagle with gl argument
-$BEAGLE_TEST gl=test.vcf.gz out=out.gl
-
-# Beagle with ref argument
+# Beagle with ref and gt argument
$BEAGLE_TEST ref=ref.vcf.gz gt=target.vcf.gz out=out.ref
-# Beagle with bref argument
-$BEAGLE_TEST ref=ref.bref gt=target.vcf.gz out=out.bref
+# Beagle with bref3 file
+$BEAGLE_TEST ref=ref.bref3 gt=target.vcf.gz out=out.bref3
rm -f $ADTTMP/*
=====================================
debian/upstream.docs/README
=====================================
@@ -1,10 +1,10 @@
# Author: Dylan Assi <bob.dybian at gmail.com>
-# Last-Update: 2016-06-17
+# Last-Update: 2018-09-16
# 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/release_notes
- wget https://faculty.washington.edu/browning/beagle/beagle_4.1_21Jan17.pdf -O beagle_4.1.pdf
- wget https://faculty.washington.edu/browning/beagle/run.beagle.08Jun17.d8b.example -O run.beagle.example
- wget https://faculty.washington.edu/browning/beagle/test.08Jun17.d8b.vcf.gz -O test.vcf.gz && \
+ wget https://faculty.washington.edu/browning/beagle/beagle5_release_notes -O release_notes
+ wget https://faculty.washington.edu/browning/beagle/beagle_5.0_07Sep18.pdf -O beagle_5.0.pdf
+ wget https://faculty.washington.edu/browning/beagle/run.beagle.15Sep18.8a0.example -O run.beagle.example
+ wget http://faculty.washington.edu/browning/beagle/test.15Sep18.8a0.vcf.gz -O test.vcf.gz && \
gunzip test.vcf.gz
=====================================
debian/upstream.docs/beagle_4.1.pdf deleted
=====================================
Binary files a/debian/upstream.docs/beagle_4.1.pdf and /dev/null differ
=====================================
debian/upstream.docs/beagle_5.0.pdf
=====================================
Binary files /dev/null and b/debian/upstream.docs/beagle_5.0.pdf differ
=====================================
debian/upstream.docs/release_notes
=====================================
@@ -1,40 +1,48 @@
-Changes in Beagle 5.0
-=========================
-* Much faster genotype phasing and genotype imputation algorithms.
-* An improved reference file format: bref3 which supersedes bref version 2.
-* Window and overlap parameters use centiMorgan units.
-* Some user parameters are changed (see documentation).
-* Refined IBD algorithm removed from Beagle and made a stand-alone program.
-* Input VCF file must contain genotype (GT) fields (GL/PL fields are ignored).
-
-Beagle 5.0 (14May18.ff7) release notes
-=============================================
-* First release of Beagle version 5.0
-
-Beagle 5.0 (16May18.771) release notes
-=============================================
-* Fixed a bug when phasing and imputing in the same analysis
-
-Beagle 5.0 (24May18.276.jar) release notes
-=============================================
-* Minor modification to phasing algorithm
-
-Beagle 5.0 (28May18.405) release notes
-=============================================
-* Fixed a concurrency bug
-
-Beagle 5.0 (30May18.3bb) release notes
-=============================================
-* Improved error messages
-
-Beagle 5.0 (04Jun18.a80) release notes
-=============================================
-* Fixed a bug in phasing when ALT field is '.'
-
-Beagle 5.0 (10Jun18.811) release notes
-=============================================
-* Fix bug appearing when there is a large inter-marker distance
-
-Beagle 5.0 (03Jul18.40b) release notes
-=============================================
-* Fixed a bug appearing when reference panel ALT field is '.'
+Changes in Beagle 5.0
+=========================
+* Much faster genotype phasing and genotype imputation algorithms.
+* An improved reference file format: bref3 which supersedes bref version 2.
+* Window and overlap parameters use centiMorgan units.
+* Some user parameters are changed (see documentation).
+* Refined IBD algorithm removed from Beagle and made a stand-alone program.
+* Input VCF file must contain genotype (GT) fields (GL/PL fields are ignored).
+
+Beagle 5.0 (14May18.ff7) release notes
+=============================================
+* First release of Beagle version 5.0
+
+Beagle 5.0 (16May18.771) release notes
+=============================================
+* Fixed a bug when phasing and imputing in the same analysis
+
+Beagle 5.0 (24May18.276.jar) release notes
+=============================================
+* Minor modification to phasing algorithm
+
+Beagle 5.0 (28May18.405) release notes
+=============================================
+* Fixed a concurrency bug
+
+Beagle 5.0 (30May18.3bb) release notes
+=============================================
+* Improved error messages
+
+Beagle 5.0 (04Jun18.a80) release notes
+=============================================
+* Fixed a bug in phasing when ALT field is '.'
+
+Beagle 5.0 (10Jun18.811) release notes
+=============================================
+* Fix bug appearing when there is a large inter-marker distance
+
+Beagle 5.0 (03Jul18.40b) release notes
+=============================================
+* Fixed a bug appearing when reference panel ALT field is '.'
+
+Beagle 5.0 (10Sep18.879) release notes
+=============================================
+* Fixed a bug in imputation output when reference panel ALT field is '.'
+
+Beagle 5.0 (15Sep18.8a0) release notes
+=============================================
+* Fixed a bug appearing when analysis window has only one target marker
=====================================
debian/upstream.docs/run.beagle.example
=====================================
@@ -1,53 +1,47 @@
#!/bin/bash
-if [ ! -f beagle.08Jun17.d8b.jar ]; then
+if [ ! -f beagle.15Sep18.8a0.jar ]; then
echo
- echo "Downloading beagle.08Jun17.d8b.jar"
- wget http://faculty.washington.edu/browning/beagle/beagle.08Jun17.d8b.jar
+ echo "Downloading beagle.15Sep18.8a0.jar"
+ wget http://faculty.washington.edu/browning/beagle/beagle.15Sep18.8a0.jar
fi
-if [ ! -f bref.08Jun17.d8b.jar ]; then
+if [ ! -f bref3.15Sep18.8a0.jar ]; then
echo
- echo "Downloading bref.08Jun17.d8b.jar"
- wget http://faculty.washington.edu/browning/beagle/bref.08Jun17.d8b.jar
+ echo "Downloading bref3.15Sep18.8a0.jar"
+ wget http://faculty.washington.edu/browning/beagle/bref3.15Sep18.8a0.jar
fi
echo
-if [ ! -f test.08Jun17.d8b.vcf.gz ]; then
+if [ ! -f test.15Sep18.8a0.vcf.gz ]; then
echo
- echo "*** Downloading some 1000 Genomes Project data to file: test.08Jun17.d8b.vcf.gz ***"
- wget http://faculty.washington.edu/browning/beagle/test.08Jun17.d8b.vcf.gz
+ echo "*** Downloading some 1000 Genomes Project data to file: test.15Sep18.8a0.vcf.gz ***"
+ wget http://faculty.washington.edu/browning/beagle/test.15Sep18.8a0.vcf.gz
fi
echo
-echo "*** Creating test files: ref.08Jun17.d8b.vcf.gz target.08Jun17.d8b.vcf.gz ***"
+echo "*** Creating test files: ref.15Sep18.8a0.vcf.gz target.15Sep18.8a0.vcf.gz ***"
echo
-zcat test.08Jun17.d8b.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.08Jun17.d8b.vcf.gz
-zcat test.08Jun17.d8b.vcf.gz | cut -f1-9,191-200 | gzip > target.08Jun17.d8b.vcf.gz
-
+zcat test.15Sep18.8a0.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.15Sep18.8a0.vcf.gz
+zcat test.15Sep18.8a0.vcf.gz | cut -f1-9,191-200 | gzip > target.15Sep18.8a0.vcf.gz
echo
echo "*** Running test analysis with \"gt=\" argument ***"
echo
-java -jar beagle.08Jun17.d8b.jar gt=test.08Jun17.d8b.vcf.gz out=out.gt
-
-echo
-echo "*** Running test analysis with \"gl=\" argument ***"
-echo
-java -jar beagle.08Jun17.d8b.jar gl=test.08Jun17.d8b.vcf.gz out=out.gl
+java -jar beagle.15Sep18.8a0.jar gt=test.15Sep18.8a0.vcf.gz out=out.gt
echo
-echo "*** Running test analysis with \"ref=\" argument ***"
+echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
echo
-java -jar beagle.08Jun17.d8b.jar ref=ref.08Jun17.d8b.vcf.gz gt=target.08Jun17.d8b.vcf.gz out=out.ref
+java -jar beagle.15Sep18.8a0.jar ref=ref.15Sep18.8a0.vcf.gz gt=target.15Sep18.8a0.vcf.gz out=out.ref
echo
-echo "*** Making \"bref\" file ***"
+echo "*** Making \"bref3\" file ***"
echo
-java -jar bref.08Jun17.d8b.jar ref.08Jun17.d8b.vcf.gz
+java -jar bref3.15Sep18.8a0.jar ref.15Sep18.8a0.vcf.gz > ref.15Sep18.8a0.bref3
echo
-echo "*** Running test analysis with \"bref=\" argument ***"
+echo "*** Running test analysis with \"bref3\" file ***"
echo
-java -jar beagle.08Jun17.d8b.jar ref=ref.08Jun17.d8b.bref gt=target.08Jun17.d8b.vcf.gz out=out.bref
+java -jar beagle.15Sep18.8a0.jar ref=ref.15Sep18.8a0.bref3 gt=target.15Sep18.8a0.vcf.gz out=out.bref3
=====================================
imp/ImputedRecBuilder.java
=====================================
@@ -261,20 +261,27 @@ public final class ImputedRecBuilder {
}
private void printInfoField(PrintWriter out, boolean isImputed) {
- for (int a=1; a<nAlleles; ++a) {
- out.print( (a==1) ? "DR2=" : Const.comma);
- out.print(R2_VALS[(int) Math.rint(100*r2(a))]);
- }
- for (int a=1; a<nAlleles; ++a) {
- out.print( (a==1) ? ";AF=" : Const.comma);
- out.print(DF4.format(sumAlProbs[a]/nHaps));
- }
- if (marker.end()!=-1) {
- out.print(";END=");
- out.print(marker.end());
+ if (nAlleles==1) {
+ if (isImputed) {
+ out.print("IMP");
+ }
}
- if (isImputed) {
- out.print(";IMP");
+ else {
+ for (int a=1; a<nAlleles; ++a) {
+ out.print( (a==1) ? "DR2=" : Const.comma);
+ out.print(R2_VALS[(int) Math.rint(100*r2(a))]);
+ }
+ for (int a=1; a<nAlleles; ++a) {
+ out.print( (a==1) ? ";AF=" : Const.comma);
+ out.print(DF4.format(sumAlProbs[a]/nHaps));
+ }
+ if (marker.end()!=-1) {
+ out.print(";END=");
+ out.print(marker.end());
+ }
+ if (isImputed) {
+ out.print(";IMP");
+ }
}
}
@@ -294,6 +301,7 @@ public final class ImputedRecBuilder {
private static String[] defaultHomRefFields() {
String[] sa = new String[5];
+ sa[1] = Const.tab + "0|0";
sa[2] = Const.tab + "0|0:0";
for (int j=3; j<sa.length; ++j) {
sa[j] = sa[j-1] + ",0";
@@ -303,7 +311,7 @@ public final class ImputedRecBuilder {
private static String[] homRefFields(boolean ap, boolean gp) {
String[] homRefField = new String[DEFAULT_HOM_REF_FIELDS.length];
- for (int nAl=2; nAl<homRefField.length; ++nAl) {
+ for (int nAl=1; nAl<homRefField.length; ++nAl) {
StringBuilder sb = new StringBuilder(DEFAULT_HOM_REF_FIELDS[nAl]);
if (ap) {
for (int a=1; a<nAl; ++a) {
=====================================
imp/ImputedVcfWriter.java
=====================================
@@ -61,7 +61,9 @@ public class ImputedVcfWriter {
* @param refEnd an upper bound (exclusive) on the reference markers
* that will be printed
* @throws IndexOutOfBoundsException if
- * {@code (minRefStart < 0 || maxRefEnd > impData.refGT().nMarkers())}
+ * {@code (refStart < 0 || refEnd > impData.refGT().nMarkers())}
+ * @throws IndexOutOfBoundsException if
+ * {@code targCluster < 0 || targCluster >= impData.nClusters()}
* @throws NullPointerException if {@code impData == null}
*/
public ImputedVcfWriter(ImpData impData, int targCluster, int refStart,
@@ -76,18 +78,16 @@ public class ImputedVcfWriter {
this.targCluster = targCluster;
if (targCluster==0) {
this.refStart = refStart;
- int tmpClustEnd = Math.max(refStart, impData.refClusterEnd(targCluster));
- this.clustEnd = Math.min(tmpClustEnd, refEnd);
- this.refEnd = Math.min(impData.refClusterStart(targCluster + 1), refEnd);
}
- else if (targCluster < impData.nClusters()-1) {
+ else {
this.refStart = Math.max(refStart, impData.refClusterStart(targCluster));
+ }
+ if (targCluster < impData.nClusters()-1) {
int tmpClustEnd = Math.max(refStart, impData.refClusterEnd(targCluster));
this.clustEnd = Math.min(tmpClustEnd, refEnd);
this.refEnd = Math.min(impData.refClusterStart(targCluster + 1), refEnd);
}
else {
- this.refStart = Math.max(refStart, impData.refClusterStart(targCluster));
this.clustEnd = refEnd;
this.refEnd = refEnd;
}
=====================================
main/Main.java
=====================================
@@ -70,8 +70,8 @@ public class Main {
* The program name and version.
*/
public static final String VERSION = "(version 5.0)";
- public static final String PROGRAM = "beagle.03Jul18.40b.jar";
- public static final String COMMAND = "java -jar beagle.03Jul18.40b.jar";
+ public static final String PROGRAM = "beagle.15Sep18.8a0.jar";
+ public static final String COMMAND = "java -jar beagle.15Sep18.8a0.jar";
/**
* The copyright string.
@@ -83,7 +83,7 @@ public class Main {
*/
public static final String SHORT_HELP = Main.PROGRAM + " " + VERSION
+ Const.nl + Main.COPYRIGHT
- + Const.nl + "Enter \"java -jar beagle.03Jul18.40b.jar\" to "
+ + Const.nl + "Enter \"java -jar beagle.15Sep18.8a0.jar\" to "
+ "list command line argument";
private final Par par;
=====================================
main/MainHelper.java
=====================================
@@ -101,7 +101,7 @@ public class MainHelper {
rand.nextLong());
long t1 = System.nanoTime();
PhaseLS.run(phaseData, estPhase, recombRegress);
- if (recombRegress!=null) {
+ if (recombRegress!=null && recombRegress.cnt()>=100) {
recombFactor = recombFactor(cd, recombRegress);
}
long elapsedNanos = System.nanoTime() - t0;
View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/a846410ba62a72e1b2f474b0fc7e895614eeb796...6bef376f6968d81946f88e8ee70f39fd0aff093f
--
View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/a846410ba62a72e1b2f474b0fc7e895614eeb796...6bef376f6968d81946f88e8ee70f39fd0aff093f
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