Merge branch 'development'

exomiser-cli/CHANGELOG.md

@@ -1,56 +1,59 @@
-# The Exomiser Command Line Executable - Changelog
-
-## 5.0.0 2014-11-14
-- New filter option --genes-to-keep  Allows filtering by Entrez gene ID to keep only those genes specified.
-- Added caching options which may significantly increase performance at the expense of memory - see application.properties.
-- Changed 'username' in application.properties to 'dbuser' to prevent the current user's username from being used to authenticate against the PostgreSQL database on Windows.
-- Added missing full-analysis option to test and example.settings
-- Updated external dependencies
-- Lots of under the hood changes and increased test coverage in exomiser-core.
-
-## 4.0.1 2014-10-23
-- Fixed bug where OMIM prioritiser did not work when inheritance model was not specified
-- Adjustment of the exomiser-allspecies algorithm for PPI hits
-
-## 4.0.0 2014-09-19
-- Changed FilterScores to FilterResults to encapsulate the pass/fail , score and filterTypes returned from the filters in various ways previously.
-- Changed Filter behaviour to simply return a FilterResult instead of altering the VariantEvaluation in inconsistent ways.
-- VariantEvaluation now hides a bit more of its inner workings regarding FilterResults.
-- PathogenicityData will now return its own most pathogenic score instead of relying on something else to figure this out.
-
-- Major changes to PathogenicityFilter behaviour - Missense variants will always pass the filter regardless of their predicted pathogenicity. Other variant types can now be filtered according to the cutoff score or allowed to pass irrespective of the score.
-- Command line option changes:
-    -P --remove-path-filter-cutoff command line option added to allow all variant types through pathogenicity filter.
-    -P --keep-non-pathogenic-missense command line option removed.
-    -P option default changed from true to false! Sorry. Check your existing settings carefully!
-
-- Added GeneFilter functionality
-- Renamed Scorable interface to Score
-- Renamed VariantEvaluation variables and accessor methods:
-    getFilterScoreMap to getFilterResults to match how it is referred to in the code output.
-    getFailedFilters to getFailedFilterTypes
-    passesFilters to passedFilters
-
-- Bug-fixes
-    - Prioritisers now release database connections when finished (affects batch-mode performance)
-    - Inheritance filter now performs correctly in all cases.
-
-#### 3.0.2 2014-09-08
-- VCF output now contains original VCF INFO field with exomiser info appended onto this.
-- Bug-fix for crash when Jannovar found no annotations for a variant.
-
-#### 3.0.1 2014-09-04
-- Bug-fix for duplicate variants in Frequency table where the RSID was different.
-
-#### 3.0.0 2014-08-22
-- Completely re-worked under the hood code
-- New extensible API
-- Simplified command-line usage
-- Multiple output formats
-- Batch mode analysis
-- Settings file input
-- Zero-config installation
-
-#### 2.1.0 2014-05-06
-- Embedded H2 database or PostgreSQL
+# The Exomiser Command Line Executable - Changelog
+
+## 5.0.1 2014-11-14
+- No changes to exomiser-cli
+
+## 5.0.0 2014-11-14
+- New filter option --genes-to-keep  Allows filtering by Entrez gene ID to keep only those genes specified.
+- Added caching options which may significantly increase performance at the expense of memory - see application.properties.
+- Changed 'username' in application.properties to 'dbuser' to prevent the current user's username from being used to authenticate against the PostgreSQL database on Windows.
+- Added missing full-analysis option to test and example.settings
+- Updated external dependencies
+- Lots of under the hood changes and increased test coverage in exomiser-core.
+
+## 4.0.1 2014-10-23
+- Fixed bug where OMIM prioritiser did not work when inheritance model was not specified
+- Adjustment of the exomiser-allspecies algorithm for PPI hits
+
+## 4.0.0 2014-09-19
+- Changed FilterScores to FilterResults to encapsulate the pass/fail , score and filterTypes returned from the filters in various ways previously.
+- Changed Filter behaviour to simply return a FilterResult instead of altering the VariantEvaluation in inconsistent ways.
+- VariantEvaluation now hides a bit more of its inner workings regarding FilterResults.
+- PathogenicityData will now return its own most pathogenic score instead of relying on something else to figure this out.
+
+- Major changes to PathogenicityFilter behaviour - Missense variants will always pass the filter regardless of their predicted pathogenicity. Other variant types can now be filtered according to the cutoff score or allowed to pass irrespective of the score.
+- Command line option changes:
+    -P --remove-path-filter-cutoff command line option added to allow all variant types through pathogenicity filter.
+    -P --keep-non-pathogenic-missense command line option removed.
+    -P option default changed from true to false! Sorry. Check your existing settings carefully!
+
+- Added GeneFilter functionality
+- Renamed Scorable interface to Score
+- Renamed VariantEvaluation variables and accessor methods:
+    getFilterScoreMap to getFilterResults to match how it is referred to in the code output.
+    getFailedFilters to getFailedFilterTypes
+    passesFilters to passedFilters
+
+- Bug-fixes
+    - Prioritisers now release database connections when finished (affects batch-mode performance)
+    - Inheritance filter now performs correctly in all cases.
+
+#### 3.0.2 2014-09-08
+- VCF output now contains original VCF INFO field with exomiser info appended onto this.
+- Bug-fix for crash when Jannovar found no annotations for a variant.
+
+#### 3.0.1 2014-09-04
+- Bug-fix for duplicate variants in Frequency table where the RSID was different.
+
+#### 3.0.0 2014-08-22
+- Completely re-worked under the hood code
+- New extensible API
+- Simplified command-line usage
+- Multiple output formats
+- Batch mode analysis
+- Settings file input
+- Zero-config installation
+
+#### 2.1.0 2014-05-06
+- Embedded H2 database or PostgreSQL
 - Simplified set-up/installation

exomiser-cli/pom.xml

@@ -11,7 +11,7 @@
     <parent>
         <groupId>de.charite.compbio</groupId>
         <artifactId>Exomiser</artifactId>
-        <version>5.0.0</version>
+        <version>5.0.1</version>
     </parent>
 
     <properties>
@@ -24,12 +24,6 @@
             <artifactId>exomiser-core</artifactId>
             <version>${project.version}</version>
         </dependency>
-        <!--Jannovar is used for providing known gene annotations on variants -->
-<!--        <dependency>
-            <groupId>de.charite.compbio</groupId>
-            <artifactId>jannovar</artifactId>
-            <version>0.9-SNAPSHOT</version>
-        </dependency>-->
         <!--commons-cli used for parsing the command line -->
         <dependency>
             <groupId>commons-cli</groupId>

exomiser-core/CHANGELOG.md

@@ -1,5 +1,8 @@
 # The Exomiser - Core Library Changelog
 
+## 5.0.1 2014-11-14
+- Changed Jannovar to version 0.9 to fix a null pointer caused by inability to translate certain variants.
+
 ## 5.0.0 2014-11-14
 - Focused on improving test coverage of the Factory and DAO packages in particular.
 - API changes:

exomiser-core/pom.xml

@@ -9,7 +9,7 @@
     <parent>    
         <groupId>de.charite.compbio</groupId>
         <artifactId>Exomiser</artifactId>
-        <version>5.0.0</version>
+        <version>5.0.1</version>
     </parent>
 
     <properties>

exomiser-db/pom.xml

@@ -11,7 +11,7 @@
     <parent>
         <groupId>de.charite.compbio</groupId>
         <artifactId>Exomiser</artifactId>
-        <version>5.0.0</version>
+        <version>5.0.1</version>
     </parent>
 
     <properties>

exomiser-web/pom.xml

@@ -10,7 +10,7 @@
     <parent>
         <artifactId>Exomiser</artifactId>
         <groupId>de.charite.compbio</groupId>
-        <version>5.0.0</version>
+        <version>5.0.1</version>
     </parent>
 
     <properties>

pom.xml

@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>de.charite.compbio</groupId>
     <artifactId>Exomiser</artifactId>
-    <version>5.0.0</version>
+    <version>5.0.1</version>
     <packaging>pom</packaging>
     <name>Exomiser</name>