{"action":"created","comment":{"url":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/comments/55115794","id":55115794,"diff_hunk":"@@ -0,0 +1,57 @@\n+/*\n+ * The MIT License\n+ *\n+ * Copyright (c) 2016 Fulcrum Genomics LLC\n+ *\n+ * Permission is hereby granted, free of charge, to any person obtaining a copy\n+ * of this software and associated documentation files (the \"Software\"), to deal\n+ * in the Software without restriction, including without limitation the rights\n+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n+ * copies of the Software, and to permit persons to whom the Software is\n+ * furnished to do so, subject to the following conditions:\n+ *\n+ * The above copyright notice and this permission notice shall be included in\n+ * all copies or substantial portions of the Software.\n+ *\n+ * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n+ * THE SOFTWARE.\n+ */package com.fulcrumgenomics.util\n+\n+import java.io.{BufferedReader, FileInputStream, InputStreamReader}\n+import java.util.zip.GZIPInputStream\n+\n+import com.fulcrumgenomics.testing.UnitSpec\n+\n+/**\n+  * Tests for the Io utility class.\n+  */\n+class IoTest extends UnitSpec {\n+\n+  \"Io\" should \"open a file for gzip writing if it ends with .gz\" in {\n+    val text = \"This is a stupid little text fragment for compression. Yay compression!\"\n+    val in   = Seq(text, text, text)\n+    val f = makeTempFile(\"test\", \".gz\")\n+    Io.writeLines(f, in)\n+\n+    // Manually read it back as gzipped data\n+    val reader = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(f.toFile))))\n+    val out = Seq(reader.readLine(), reader.readLine(), reader.readLine())\n+    out shouldBe in\n+  }\n+\n+  \"Io\" should \"round trip data to a gzipped file if it ends with .gz\" in {\n+    val text = \"This is a stupid little text fragment for compression. Yay compression!\"\n+    val in   = Seq(text, text, text)\n+    val f = makeTempFile(\"test\", \".gz\")\n+    Io.writeLines(f, in)\n+    val out = Io.readLines(f).toSeq\n+    out shouldBe in\n+  }\n+\n+","path":"src/test/scala/com/fulcrumgenomics/util/IoTest.scala","position":56,"original_position":56,"commit_id":"f6558919f1a574cdd18d4e716a6e1bbef166145d","original_commit_id":"f6558919f1a574cdd18d4e716a6e1bbef166145d","user":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"body":"I was about to ask","created_at":"2016-03-05T05:03:18Z","updated_at":"2016-03-05T05:03:18Z","html_url":"https://github.com/fulcrumgenomics/fgbio/pull/10#discussion_r55115794","pull_request_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/10","_links":{"self":{"href":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/comments/55115794"},"html":{"href":"https://github.com/fulcrumgenomics/fgbio/pull/10#discussion_r55115794"},"pull_request":{"href":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/10"}}},"pull_request":{"url":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/10","id":61708292,"html_url":"https://github.com/fulcrumgenomics/fgbio/pull/10","diff_url":"https://github.com/fulcrumgenomics/fgbio/pull/10.diff","patch_url":"https://github.com/fulcrumgenomics/fgbio/pull/10.patch","issue_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/issues/10","number":10,"state":"open","locked":false,"title":"First cut at a more idiomatic scala fastq reader.","user":{"login":"tfenne","id":1609210,"avatar_url":"https://avatars.githubusercontent.com/u/1609210?v=3","gravatar_id":"","url":"https://api.github.com/users/tfenne","html_url":"https://github.com/tfenne","followers_url":"https://api.github.com/users/tfenne/followers","following_url":"https://api.github.com/users/tfenne/following{/other_user}","gists_url":"https://api.github.com/users/tfenne/gists{/gist_id}","starred_url":"https://api.github.com/users/tfenne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tfenne/subscriptions","organizations_url":"https://api.github.com/users/tfenne/orgs","repos_url":"https://api.github.com/users/tfenne/repos","events_url":"https://api.github.com/users/tfenne/events{/privacy}","received_events_url":"https://api.github.com/users/tfenne/received_events","type":"User","site_admin":false},"body":"@nh13 This isn't quite read for prime time, because it won't automatically handle `.gz` fastq file which is obviously needed.  We either need to implement `.gz` auto-handling in dagr-commons `Io`, or do something different in fgbio.  Thoughts?","created_at":"2016-03-04T12:54:49Z","updated_at":"2016-03-05T05:03:18Z","closed_at":null,"merged_at":null,"merge_commit_sha":"c75fb13ef98fb38fba8bd92b26287a90563eace3","assignee":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/10/commits","review_comments_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/10/comments","review_comment_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/comments{/number}","comments_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/issues/10/comments","statuses_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/statuses/f6558919f1a574cdd18d4e716a6e1bbef166145d","head":{"label":"fulcrumgenomics:tf_fastq_reader","ref":"tf_fastq_reader","sha":"f6558919f1a574cdd18d4e716a6e1bbef166145d","user":{"login":"fulcrumgenomics","id":13546013,"avatar_url":"https://avatars.githubusercontent.com/u/13546013?v=3","gravatar_id":"","url":"https://api.github.com/users/fulcrumgenomics","html_url":"https://github.com/fulcrumgenomics","followers_url":"https://api.github.com/users/fulcrumgenomics/followers","following_url":"https://api.github.com/users/fulcrumgenomics/following{/other_user}","gists_url":"https://api.github.com/users/fulcrumgenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/fulcrumgenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fulcrumgenomics/subscriptions","organizations_url":"https://api.github.com/users/fulcrumgenomics/orgs","repos_url":"https://api.github.com/users/fulcrumgenomics/repos","events_url":"https://api.github.com/users/fulcrumgenomics/events{/privacy}","received_events_url":"https://api.github.com/users/fulcrumgenomics/received_events","type":"Organization","site_admin":false},"repo":{"id":53011104,"name":"fgbio","full_name":"fulcrumgenomics/fgbio","owner":{"login":"fulcrumgenomics","id":13546013,"avatar_url":"https://avatars.githubusercontent.com/u/13546013?v=3","gravatar_id":"","url":"https://api.github.com/users/fulcrumgenomics","html_url":"https://github.com/fulcrumgenomics","followers_url":"https://api.github.com/users/fulcrumgenomics/followers","following_url":"https://api.github.com/users/fulcrumgenomics/following{/other_user}","gists_url":"https://api.github.com/users/fulcrumgenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/fulcrumgenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fulcrumgenomics/subscriptions","organizations_url":"https://api.github.com/users/fulcrumgenomics/orgs","repos_url":"https://api.github.com/users/fulcrumgenomics/repos","events_url":"https://api.github.com/users/fulcrumgenomics/events{/privacy}","received_events_url":"https://api.github.com/users/fulcrumgenomics/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/fulcrumgenomics/fgbio","description":"","fork":false,"url":"https://api.github.com/repos/fulcrumgenomics/fgbio","forks_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/forks","keys_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/keys{/key_id}","collaborators_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/teams","hooks_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/hooks","issue_events_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/issues/events{/number}","events_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/events","assignees_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/assignees{/user}","branches_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/branches{/branch}","tags_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/tags","blobs_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/git/refs{/sha}","trees_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/git/trees{/sha}","statuses_url":"https://api.github.com/repos/fulcrumgeno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