diff --git a/Readme.md b/Readme.md index a454c42..eb6a9a0 100644 --- a/Readme.md +++ b/Readme.md @@ -1,7 +1,10 @@ [![Bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://bioconda.github.io/recipes/vardict-java/README.html) [![European Galaxy server](https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,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)](https://usegalaxy.eu/root?tool_id=vardict_java) -> This is the Final Version of VarDict. No longer maintained. +This is a forked Version based on the original VarDict-Java 1.8.3 (the latest release produced). +The intent of this fork is *not* to add new functionalty but just to do some basic maintenance of otherwise no longer +supported valuable piece of software. This encompasses fixing security vulnerabilities and perhaps fix some +"show stopper" bugs as these araise. # VarDictJava diff --git a/build.gradle b/build.gradle index 15a6368..d1dc2b4 100644 --- a/build.gradle +++ b/build.gradle @@ -4,10 +4,10 @@ plugins { id 'jacoco' } -version = '1.8.3' +version = '1.8.3.1' repositories { - mavenCentral() + maven { url "https://repo.maven.apache.org/maven2" } } targetCompatibility = "1.8" @@ -25,11 +25,18 @@ dependencies { compile 'commons-cli:commons-cli:1.2' compile 'org.apache.commons:commons-math3:3.6.1' compile 'com.edropple.jregex:jregex:1.2_01' - compile('com.github.samtools:htsjdk:2.21.1') { + compile('com.github.samtools:htsjdk:3.0.5') { transitive = false } + // explicit commons-compress and snappy-java depenencies to force the use ot vulnerability free + // version of this packages. + compile 'org.apache.commons:commons-compress:1.26.1' + compile 'org.xerial.snappy:snappy-java:1.1.10.7' + testCompile 'org.mockito:mockito-core:2.23.0' testCompile 'org.testng:testng:6.9.13.6' + // explicit ant dependency added to force upgrade to safe version for this testng dependency. + testCompile 'org.apache.ant:ant:1.10.15' } mainClassName = "com.astrazeneca.vardict.Main" diff --git a/changelog.txt b/changelog.txt index 82f4f0e..41bb18f 100644 --- a/changelog.txt +++ b/changelog.txt @@ -1,3 +1,11 @@ +Version 1.8.3.1 + - Updated htsjdk dependency to 3.0.5 + - Upgrade transitive dependencies with vulneravilities to safe later versions: + - org.apache.commons:commons-compress (-> 1.26.1) + - org.xerial.snappy:snappy-java (-> 1.1.10.7) + - org.apache.ant:ant (-> 1.10.15) + - Deleted previous release binaries from source tree. + Version 1.8.3 - Updated submodule and version. - Fixed check for introns for the case when deletion is next to insertion. diff --git a/dist/VarDict-1.2.2.zip b/dist/VarDict-1.2.2.zip deleted file mode 100644 index acf09a4..0000000 Binary files a/dist/VarDict-1.2.2.zip and /dev/null differ diff --git a/dist/VarDict-1.2.4.zip b/dist/VarDict-1.2.4.zip deleted file mode 100644 index 23ce157..0000000 Binary files a/dist/VarDict-1.2.4.zip and /dev/null differ diff --git a/dist/VarDict-1.3.zip b/dist/VarDict-1.3.zip deleted file mode 100644 index d9c023e..0000000 Binary files a/dist/VarDict-1.3.zip and /dev/null differ diff --git a/dist/VarDict-1.4.1.zip b/dist/VarDict-1.4.1.zip deleted file mode 100644 index b527948..0000000 Binary files a/dist/VarDict-1.4.1.zip and /dev/null differ diff --git a/dist/VarDict-1.4.2.zip b/dist/VarDict-1.4.2.zip deleted file mode 100644 index e6e229d..0000000 Binary files a/dist/VarDict-1.4.2.zip and /dev/null differ diff --git a/dist/VarDict-1.4.3.zip b/dist/VarDict-1.4.3.zip deleted file mode 100644 index 446fc8a..0000000 Binary files a/dist/VarDict-1.4.3.zip and /dev/null differ diff --git a/dist/VarDict-1.4.4.zip b/dist/VarDict-1.4.4.zip deleted file mode 100644 index 02fa35a..0000000 Binary files a/dist/VarDict-1.4.4.zip and /dev/null differ diff --git a/dist/VarDict-1.4.5.zip b/dist/VarDict-1.4.5.zip deleted file mode 100644 index dfbdb1c..0000000 Binary files a/dist/VarDict-1.4.5.zip and /dev/null differ diff --git a/dist/VarDict-1.4.6.zip b/dist/VarDict-1.4.6.zip deleted file mode 100644 index 7c07aa7..0000000 Binary files a/dist/VarDict-1.4.6.zip and /dev/null differ diff --git a/dist/VarDict-1.4.7.zip b/dist/VarDict-1.4.7.zip deleted file mode 100644 index d31712c..0000000 Binary files a/dist/VarDict-1.4.7.zip and /dev/null differ diff --git a/dist/VarDict-1.4.8.zip b/dist/VarDict-1.4.8.zip deleted file mode 100644 index 1c3105c..0000000 Binary files a/dist/VarDict-1.4.8.zip and /dev/null differ diff --git a/dist/VarDict-1.4.zip b/dist/VarDict-1.4.zip deleted file mode 100644 index fb52a96..0000000 Binary files a/dist/VarDict-1.4.zip and /dev/null differ diff --git a/dist/VarDict-1.5.5.tar b/dist/VarDict-1.5.5.tar deleted file mode 100644 index eb8baac..0000000 Binary files a/dist/VarDict-1.5.5.tar and /dev/null differ diff --git a/dist/VarDict-1.5.5.zip b/dist/VarDict-1.5.5.zip deleted file mode 100644 index 972ac33..0000000 Binary files a/dist/VarDict-1.5.5.zip and /dev/null differ diff --git a/dist/VarDict-1.6.0.tar b/dist/VarDict-1.6.0.tar deleted file mode 100644 index 2c3411f..0000000 Binary files a/dist/VarDict-1.6.0.tar and /dev/null differ diff --git a/dist/VarDict-1.6.0.zip b/dist/VarDict-1.6.0.zip deleted file mode 100644 index 67dc08b..0000000 Binary files a/dist/VarDict-1.6.0.zip and /dev/null differ diff --git a/dist/VarDict-1.7.0.tar b/dist/VarDict-1.7.0.tar deleted file mode 100644 index 51a22ac..0000000 Binary files a/dist/VarDict-1.7.0.tar and /dev/null differ diff --git a/dist/VarDict-1.7.0.zip b/dist/VarDict-1.7.0.zip deleted file mode 100644 index 7fe547d..0000000 Binary files a/dist/VarDict-1.7.0.zip and /dev/null differ diff --git a/dist/VarDict-1.8.0.tar b/dist/VarDict-1.8.0.tar deleted file mode 100644 index ff3d517..0000000 Binary files a/dist/VarDict-1.8.0.tar and /dev/null differ diff --git a/dist/VarDict-1.8.0.zip b/dist/VarDict-1.8.0.zip deleted file mode 100644 index 3f70d53..0000000 Binary files a/dist/VarDict-1.8.0.zip and /dev/null differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 329ce2f..cde253a 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-4.10.2-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-6.9.3-bin.zip