From 911ffe68d68927888a9fce1634b4be16e698cf46 Mon Sep 17 00:00:00 2001
From: Walter <walterxie@users.noreply.github.com>
Date: Wed, 30 Oct 2024 16:49:24 +1300
Subject: [PATCH] Draft release 1.2.1 #69

---
 phylonco-beast/pom.xml                         | 2 +-
 phylonco-beast/version.xml                     | 2 +-
 phylonco-lphy-studio/pom.xml                   | 2 +-
 phylonco-lphy/examples/gt16ReadCountModel.lphy | 5 +++--
 phylonco-lphy/pom.xml                          | 2 +-
 phylonco-lphybeast/pom.xml                     | 2 +-
 phylonco-lphybeast/version.xml                 | 4 ++--
 pom.xml                                        | 4 ++--
 8 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/phylonco-beast/pom.xml b/phylonco-beast/pom.xml
index 1985f0a..5783cfe 100644
--- 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
index 8153b23..bb70adb 100644
--- 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
index 3b84dcb..19c76a5 100644
--- 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
index 7246717..03becc4 100644
--- 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
index d21ca21..536e941 100644
--- 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
index 2a57f75..ba83160 100644
--- 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
index 5506329..b03d331 100644
--- 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
index 05a4310..65b1797 100644
--- 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>