{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/69596386","id":69596386,"diff_hunk":"@@ -0,0 +1,91 @@\n+package org.broadinstitute.hellbender.utils.downsampling;\n+\n+import org.broadinstitute.hellbender.utils.Utils;\n+import org.broadinstitute.hellbender.utils.read.GATKRead;\n+\n+import java.util.Collection;\n+import java.util.Iterator;\n+import java.util.NoSuchElementException;\n+\n+/**\n+ * Iterator wrapper around our generic {@link ReadsDownsampler)} interface. Converts the push-style\n+ * downsampler interface to a pull model.\n+ */\n+public final class ReadsDownsamplingIterator implements Iterator<GATKRead>, Iterable<GATKRead> {\n+\n+    private final Iterator<GATKRead> nestedReadIterator;\n+    private final ReadsDownsampler downsampler;\n+    private Collection<GATKRead> downsampledReadsCache;\n+    private GATKRead nextRead = null;\n+    private Iterator<GATKRead> downsampledReadsCacheIterator = null;\n+\n+    /**\n+     * @param iter wrapped iterator from which this iterator will pull reads","path":"src/main/java/org/broadinstitute/hellbender/utils/downsampling/ReadsDownsamplingIterator.java","position":23,"original_position":23,"commit_id":"c067e1a0e6e91d6af18ead26a214f0a972e18e75","original_commit_id":"c067e1a0e6e91d6af18ead26a214f0a972e18e75","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":"A simple description of what this iterator does (in the class doc) would be sufficient here. Something that says that this is an decorator of iterators and takes a iterator and downsamples reads using the given downsampler. ","created_at":"2016-07-05T16:39:13Z","updated_at":"2016-07-05T16:39:13Z","html_url":"https://github.com/broadinstitute/gatk/pull/1972#discussion_r69596386","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1972","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/69596386"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/1972#discussion_r69596386"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/1972"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1972","id":76025033,"html_url":"https://github.com/broadinstitute/gatk/pull/1972","diff_url":"https://github.com/broadinstitute/gatk/pull/1972.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/1972.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1972","number":1972,"state":"open","locked":false,"title":"Part 1 of HC memory fixes: add downsampling to AssemblyRegion traversal","user":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"body":"-Hooked up a new PositionalDownsampler to AssemblyRegionWalker controlled\r\n via an argument --maxReadsPerAlignmentStart (tool sets the default value).\r\n\r\n-As a side effect, exposed the \"assigned\" position of a read in the\r\n GATKRead interface. This lets us query the nominal positions of unmapped\r\n reads that have been assigned a position for sorting purposes.\r\n\r\n-As a second side effect, modified ReadCoordinateComparator to sort\r\n unmapped reads with positions in the correct bam/sam file order.\r\n\r\nResolves #1642\r\nResolves 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