{"action":"created","comment":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/comments/44454079","id":44454079,"diff_hunk":"@@ -0,0 +1,79 @@\n+/*\n+ * The MIT License\n+ *\n+ * Copyright (c) 2015 Tim Fennell\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+ */\n+package htsjdk.samtools;\n+\n+import java.util.Iterator;\n+import java.util.List;\n+import java.util.Set;\n+\n+/**\n+ * A DownsamplingIterator that combines the ConstantMemory and HighAccuracy downsampling techniques to provide an\n+ * iterator that has accuracy approaching that of HighAccuracy, but with more limited memory usage.  Instead of\n+ * requiring memory proportional to number of read names in the incoming stream of reads, requires memory\n+ * approximately proportional to the number of output reads.\n+ *\n+ * @author Tim Fennell\n+ */\n+class ChainedDownsamplingIterator extends HighAccuracyDownsamplingIterator {\n+\n+    /**\n+     * Constructs a chained iterator that will read from the provided iterator and attempt to downsampling to the provided proportion.\n+     */\n+    ChainedDownsamplingIterator(final Iterator<SAMRecord> iterator, final double proportion, final int seed) {\n+        super(new ConstantMemoryDownsamplingIterator(iterator, Math.min(1, proportion + 0.01), seed), proportion, seed);","path":"src/java/htsjdk/samtools/ChainedDownsamplingIterator.java","position":44,"original_position":44,"commit_id":"2d9b732704ddfbef231100ecbc312bd8e00bcc9e","original_commit_id":"2d9b732704ddfbef231100ecbc312bd8e00bcc9e","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":"Thanks - will change.  I was kind of hoping you'd tell me the right math to use here ;)  Incidentally, why 5sd and not 4 or 6?","created_at":"2015-11-10T19:39:43Z","updated_at":"2015-11-10T19:39:43Z","html_url":"https://github.com/samtools/htsjdk/pull/372#discussion_r44454079","pull_request_url":"https://api.github.com/repos/samtools/htsjdk/pulls/372","_links":{"self":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/comments/44454079"},"html":{"href":"https://github.com/samtools/htsjdk/pull/372#discussion_r44454079"},"pull_request":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/372"}}},"pull_request":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/372","id":50003186,"html_url":"https://github.com/samtools/htsjdk/pull/372","diff_url":"https://github.com/samtools/htsjdk/pull/372.diff","patch_url":"https://github.com/samtools/htsjdk/pull/372.patch","issue_url":"https://api.github.com/repos/samtools/htsjdk/issues/372","number":372,"state":"open","locked":false,"title":"Changes 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