{"action":"created","issue":{"url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/74","repository_url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict","labels_url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/74/labels{/name}","comments_url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/74/comments","events_url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/74/events","html_url":"https://github.com/AstraZeneca-NGS/VarDict/issues/74","id":344396188,"node_id":"MDU6SXNzdWUzNDQzOTYxODg=","number":74,"title":"Difficulties in VarDict-1.5.4 installation","user":{"login":"macko-tipor","id":41622295,"node_id":"MDQ6VXNlcjQxNjIyMjk1","avatar_url":"https://avatars2.githubusercontent.com/u/41622295?v=4","gravatar_id":"","url":"https://api.github.com/users/macko-tipor","html_url":"https://github.com/macko-tipor","followers_url":"https://api.github.com/users/macko-tipor/followers","following_url":"https://api.github.com/users/macko-tipor/following{/other_user}","gists_url":"https://api.github.com/users/macko-tipor/gists{/gist_id}","starred_url":"https://api.github.com/users/macko-tipor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/macko-tipor/subscriptions","organizations_url":"https://api.github.com/users/macko-tipor/orgs","repos_url":"https://api.github.com/users/macko-tipor/repos","events_url":"https://api.github.com/users/macko-tipor/events{/privacy}","received_events_url":"https://api.github.com/users/macko-tipor/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-07-25T11:01:51Z","updated_at":"2018-07-25T12:16:46Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\n\r\nI tried to upgrade VarDict-1.5.1 to VarDict-1.5.4 to take advantage of options -u and -UN.\r\nBut I have some difficulties with VarDict-1.5.4 installation.\r\n\r\nI followed the commands included in the Readme.md document.\r\n\r\ngit clone --recursive https://github.com/AstraZeneca-NGS/VarDictJava.git\r\ncd ~/VarDictJava\r\n./gradlew clean installDist\r\n\r\nThe following error message was shown:\r\n\r\n        Downloading https://services.gradle.org/distributions/gradle-4.8-bin.zip\r\n        Exception in thread \"main\" java.net.ConnectException: Connection timed out (Connection timed out)\r\n\t        at java.net.PlainSocketImpl.socketConnect(Native Method)\r\n\t        at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)\r\n\t        at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)\r\n\t        at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)\r\n\t        at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)\r\n\t        at java.net.Socket.connect(Socket.java:589)\r\n\t        at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:673)\r\n\t        at sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:173)\r\n\t        at sun.net.NetworkClient.doConnect(NetworkClient.java:180)\r\n\t        at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)\r\n\t        at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)\r\n\t        at sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:264)\r\n\t        at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:367)\r\n\t        at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191)\r\n\t        at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)\r\n\t        at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)\r\n\t        at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177)\r\n\t        at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1564)\r\n\t        at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)\r\n\t        at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:263)\r\n\t        at org.gradle.wrapper.Download.downloadInternal(Download.java:58)\r\n\t        at org.gradle.wrapper.Download.download(Download.java:44)\r\n\t        at org.gradle.wrapper.Install$1.call(Install.java:61)\r\n\t        at org.gradle.wrapper.Install$1.call(Install.java:48)\r\n\t        at org.gradle.wrapper.ExclusiveFileAccessManager.access(ExclusiveFileAccessManager.java:65)\r\n\t        at org.gradle.wrapper.Install.createDist(Install.java:48)\r\n\t        at org.gradle.wrapper.WrapperExecutor.execute(WrapperExecutor.java:128)\r\n\t        at org.gradle.wrapper.GradleWrapperMain.main(GradleWrapperMain.java:61)\r\n\r\n\r\nI got the same message when trying:\r\n./gradlew distZip\r\n\r\nThen I installed gradle-4.9, added the gradle-4.9/bin folder to the PATH and repeated the ./gradlew clean installDist command.\r\nThe same error message was shown again.\r\n\r\n\r\nTherefore, I tried a different way.\r\nI downloaded VarDict-1.5.4.zip, created an install folder in VarDictJava folder, and unzipped VarDict-1.5.4.zip there. The bin and lib folders were created.\r\nI have successfully used VarDict-1.5.1 in the same way so far.\r\nHowever, when I tried to use VarDict-1.5.4, the following error message came:\r\n\r\n        java.util.concurrent.ExecutionException: java.lang.StringIndexOutOfBoundsException: String index out of range: -1\r\n\t        at java.util.concurrent.FutureTask.report(FutureTask.java:122)\r\n\t        at java.util.concurrent.FutureTask.get(FutureTask.java:192)\r\n\t        at com.astrazeneca.vardict.VarDict.somaticParallel(VarDict.java:394)\r\n\t        at com.astrazeneca.vardict.VarDict.nonAmpVardict(VarDict.java:301)\r\n\t        at com.astrazeneca.vardict.VarDict.start(VarDict.java:80)\r\n\t        at com.astrazeneca.vardict.Main.run(Main.java:159)\r\n\t        at com.astrazeneca.vardict.Main.main(Main.java:31)\r\n        Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -1\r\n\t        at java.lang.String.charAt(String.java:658)\r\n\t        at com.astrazeneca.vardict.VarDict.isHasAndNotEquals(VarDict.java:4422)\r\n\t        at com.astrazeneca.vardict.VarDict.modifyCigar(VarDict.java:6825)\r\n\t        at com.astrazeneca.vardict.VarDict.parseSAM(VarDict.java:1673)\r\n\t        at com.astrazeneca.vardict.VarDict.toVars(VarDict.java:2917)\r\n\t        at com.astrazeneca.vardict.VarDict$ToVarsWorker.call(VarDict.java:5753)\r\n\t        at com.astrazeneca.vardict.VarDict$SomdictWorker.call(VarDict.java:5774)\r\n\t        at com.astrazeneca.vardict.VarDict$SomdictWorker.call(VarDict.java:5758)\r\n\t        at java.util.concurrent.FutureTask.run(FutureTask.java:266)\r\n\t        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)\r\n\t        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)\r\n\t        at java.lang.Thread.run(Thread.java:748)\r\n\r\nI repeated the installation steps with VarDict-1.5.3 and VarDict-1.5.2.\r\nI got the same error message when trying to run VarDict-1.5.3.\r\nOn the contrary, VarDict-1.5.2 works well.\r\n\r\nNow I can apply VarDict-1.5.2 which includes the -u and -UN options.\r\nBut what can I do to install the latest version?\r\n\r\nMy java version is 1.8.0_171.\r\n\r\n\r\nThank you very much for your help!\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/comments/407734594","html_url":"https://github.com/AstraZeneca-NGS/VarDict/issues/74#issuecomment-407734594","issue_url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/74","id":407734594,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNzczNDU5NA==","user":{"login":"mjafin","id":3286525,"node_id":"MDQ6VXNlcjMyODY1MjU=","avatar_url":"https://avatars0.githubusercontent.com/u/3286525?v=4","gravatar_id":"","url":"https://api.github.com/users/mjafin","html_url":"https://github.com/mjafin","followers_url":"https://api.github.com/users/mjafin/followers","following_url":"https://api.github.com/users/mjafin/following{/other_user}","gists_url":"https://api.github.com/users/mjafin/gists{/gist_id}","starred_url":"https://api.github.com/users/mjafin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mjafin/subscriptions","organizations_url":"https://api.github.com/users/mjafin/orgs","repos_url":"https://api.github.com/users/mjafin/repos","events_url":"https://api.github.com/users/mjafin/events{/privacy}","received_events_url":"https://api.github.com/users/mjafin/received_events","type":"User","site_admin":false},"created_at":"2018-07-25T12:16:46Z","updated_at":"2018-07-25T12:16:46Z","author_association":"CONTRIBUTOR","body":"Hi @macko-tipor,\r\nCould you try the ready built jars from https://github.com/AstraZeneca-NGS/VarDictJava/releases ?"}}
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