Draft release 1.2.1 #69

bioDS · Oct 30, 2024 · 911ffe6 · 911ffe6
1 parent 2ec6f5b
commit 911ffe6
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Showing 8 changed files with 12 additions and 11 deletions.
diff --git a/phylonco-beast/pom.xml b/phylonco-beast/pom.xml
@@ -9,7 +9,7 @@
 
     <artifactId>phylonco-beast</artifactId>
     <!-- phylonco-beast version, it must be consisting with version.xml   -->
-    <version>1.2.0</version>
+    <version>1.2.1</version>
 
     <properties>
         <!-- it must be consisting with version.xml, and the jar names in the lib folder -->

diff --git a/phylonco-beast/version.xml b/phylonco-beast/version.xml
@@ -1,4 +1,4 @@
-<package name='phylonco' version='1.2.0'>
+<package name='phylonco' version='1.2.1'>
     <!-- phylonco beast -->
     <depends on='BEAST.base' atleast='2.7.6'/>
     <depends on='BEAST.app' atleast='2.7.6'/>

diff --git a/phylonco-lphy-studio/pom.xml b/phylonco-lphy-studio/pom.xml
@@ -7,7 +7,7 @@
     </parent>
 
     <artifactId>phylonco-lphy-studio</artifactId>
-    <version>1.2.0</version>
+    <version>1.2.1</version>
 
     <dependencies>
         <dependency>

diff --git a/phylonco-lphy/examples/gt16ReadCountModel.lphy b/phylonco-lphy/examples/gt16ReadCountModel.lphy
@@ -1,6 +1,6 @@
 data {
-n = 6;
-l = 10;
+n = 10;
+l = 500;
 w1 = 10.0;
 epsilon = 0.1; // try 0.5
 delta = 0.2;
@@ -10,6 +10,7 @@ meanV = 0.1; // variance coverage = lognormal(meanV, sdV)
 sdV = 0.05;
 meanS = 1.2; // cell-specific scaling
 sdS = 0.2;
+A = readNexus(file="/Users/dxie004/WorkSpace/beast-phylonco/phylonco-lphy/examples/data/gt16ReadCountModel_A.nexus");
 }
 
 model {

diff --git a/phylonco-lphy/pom.xml b/phylonco-lphy/pom.xml
@@ -8,7 +8,7 @@
     </parent>
 
     <artifactId>phylonco-lphy</artifactId>
-    <version>1.2.0</version>
+    <version>1.2.1</version>
 
     <dependencies>
         <dependency>

diff --git a/phylonco-lphybeast/pom.xml b/phylonco-lphybeast/pom.xml
@@ -8,7 +8,7 @@
 
     <artifactId>phylonco-lphybeast</artifactId>
     <!-- phylonco-lphybeast version, it must be consisting with version.xml   -->
-    <version>1.2.0</version>
+    <version>1.2.1</version>
 
     <dependencies>
 <!--        <dependency>-->

diff --git a/phylonco-lphybeast/version.xml b/phylonco-lphybeast/version.xml
@@ -1,7 +1,7 @@
-<package name='phylonco.lphybeast' version='1.2.0'>
+<package name='phylonco.lphybeast' version='1.2.1'>
     <!-- phylonco beast -->
     <depends on='phylonco' atleast='1.2.0'/>
-    <depends on='lphybeast' atleast='1.2.0'/>
+    <depends on='lphybeast' atleast='1.2.1'/>
 
     <!--  include lphybeast  -->
     <depends on='lphybeast-flc' atleast='0.0.1'/>

diff --git a/pom.xml b/pom.xml
@@ -19,12 +19,12 @@
 
     <properties>
         <lphy.vision>1.6.1</lphy.vision>
-<!--        <lphybeast.vision>1.2.0-SNAPSHOT</lphybeast.vision>-->
+        <lphybeast.vision>1.2.1</lphybeast.vision>
 <!--  include lphybeast  -->
         <lphybeast.flc.vision>0.0.1-SNAPSHOT</lphybeast.flc.vision>
         <!-- phylonco pom version https://maven.apache.org/maven-ci-friendly.html -->
         <!-- change version in phylonco-beast or phylonco-lphybeast pom, not here  -->
-        <revision>1.2.0</revision>
+        <revision>1.2.1</revision>
         <maven.compiler.source>17</maven.compiler.source>
         <maven.compiler.target>17</maven.compiler.target>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>