{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/59987213","id":59987213,"diff_hunk":"@@ -0,0 +1,124 @@\n+package org.broadinstitute.hellbender.tools.spark.sv;\n+\n+import com.google.common.annotations.VisibleForTesting;\n+\n+import java.io.BufferedReader;\n+import java.io.File;\n+import java.io.IOException;\n+import java.io.InputStreamReader;\n+import java.util.ArrayList;\n+\n+/**\n+ * A class for experimenting with cmd line programs (such as bwa and sga) that's not part of GATK (or has Java bindings yet).\n+ */\n+public abstract class CMDLineProgramModule {\n+\n+    public CMDLineProgramModule(){  }\n+\n+    /**\n+     * Builds the initial argument list for the command line (e.g. \"bwa mem\").\n+     * @return a list of strings having the names of requested tools.\n+     * @throws IOException\n+     */\n+    abstract ArrayList<String> initializeCommands() throws IOException;","path":"src/main/java/org/broadinstitute/hellbender/tools/spark/sv/CMDLineProgramModule.java","position":23,"original_position":23,"commit_id":"e8a4fe5a2be4a1adfb9c4f0d316cda653e4022c4","original_commit_id":"e8a4fe5a2be4a1adfb9c4f0d316cda653e4022c4","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"body":"all Lists have an order. I was suggesting replacing `abstract ArrayList<String>` with `abstract List<String> `","created_at":"2016-04-17T16:00:05Z","updated_at":"2016-04-17T16:00:05Z","html_url":"https://github.com/broadinstitute/gatk/pull/1701#discussion_r59987213","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1701","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/59987213"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/1701#discussion_r59987213"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/1701"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1701","id":66094544,"html_url":"https://github.com/broadinstitute/gatk/pull/1701","diff_url":"https://github.com/broadinstitute/gatk/pull/1701.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/1701.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1701","number":1701,"state":"open","locked":false,"title":"Dummy demo of BWA-MEM call via process builder (Review & NO merge)","user":{"login":"SHuang-Broad","id":16310888,"avatar_url":"https://avatars.githubusercontent.com/u/16310888?v=3","gravatar_id":"","url":"https://api.github.com/users/SHuang-Broad","html_url":"https://github.com/SHuang-Broad","followers_url":"https://api.github.com/users/SHuang-Broad/followers","following_url":"https://api.github.com/users/SHuang-Broad/following{/other_user}","gists_url":"https://api.github.com/users/SHuang-Broad/gists{/gist_id}","starred_url":"https://api.github.com/users/SHuang-Broad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SHuang-Broad/subscriptions","organizations_url":"https://api.github.com/users/SHuang-Broad/orgs","repos_url":"https://api.github.com/users/SHuang-Broad/repos","events_url":"https://api.github.com/users/SHuang-Broad/events{/privacy}","received_events_url":"https://api.github.com/users/SHuang-Broad/received_events","type":"User","site_admin":false},"body":"Hi Adam, \r\n\r\nThis is close-to-minimal 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