{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/76805230","id":76805230,"diff_hunk":"@@ -0,0 +1,38 @@\n+package org.broadinstitute.hellbender.utils.samples;\n+\n+import org.broadinstitute.hellbender.exceptions.UserException;\n+import org.broadinstitute.hellbender.utils.text.XReadLines;\n+\n+import java.io.File;\n+import java.io.IOException;\n+import java.util.Collection;\n+import java.util.LinkedHashSet;\n+import java.util.List;\n+import java.util.Set;\n+import java.util.stream.Collectors;\n+\n+/**\n+ * Sample utilities class.\n+ */\n+public class SampleUtils {\n+    /**\n+     * Given a list of files with sample names it reads all files and creates a list of unique samples from all these files.\n+     * @param files list of files with sample names in\n+     * @return a collection of unique samples from all files\n+     */\n+    public static Collection<String> getSamplesFromFiles (Collection<File> files) {","path":"src/main/java/org/broadinstitute/hellbender/utils/samples/SampleUtils.java","position":23,"original_position":23,"commit_id":"5cd9ac71ee9a5538b26e8812f2e2b741ff5d7264","original_commit_id":"5cd9ac71ee9a5538b26e8812f2e2b741ff5d7264","user":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars.githubusercontent.com/u/10062863?v=3","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"body":"Done.","created_at":"2016-08-30T14:25:42Z","updated_at":"2016-08-30T14:25:42Z","html_url":"https://github.com/broadinstitute/gatk/pull/2094#discussion_r76805230","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/2094","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/76805230"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/2094#discussion_r76805230"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/2094"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/2094","id":81475358,"html_url":"https://github.com/broadinstitute/gatk/pull/2094","diff_url":"https://github.com/broadinstitute/gatk/pull/2094.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/2094.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2094","number":2094,"state":"open","locked":false,"title":"VariantRecalibrator and ApplyVQSR port part 1 (no integration tests).","user":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars.githubusercontent.com/u/10062863?v=3","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"body":"The first commit has the raw GATK3 files, the second has the ported files. 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