{"action":"created","comment":{"url":"https://api.github.com/repos/hammerlab/guacamole/pulls/comments/58218719","id":58218719,"diff_hunk":"@@ -79,14 +79,13 @@ object GermlineAssemblyCaller {\n      * @param reads  Set of reads to extract sequence from\n      * @param startLocus Start (inclusive) locus on the reference\n      * @param endLocus End (exclusive) locus on the reference\n-     * @param kmerSize Length of the subsequence\n      * @param minOccurrence Mininum number of times a subsequence needs to appear to be included\n      * @return List of subsequences overlapping [startLocus, endLocus) that appear at least `minOccurrence` time\n      */\n     def getConsensusKmer(reads: Seq[MappedRead],\n                          startLocus: Int,\n                          endLocus: Int,\n-                         minOccurrence: Int): Iterable[Array[Byte]] = {\n+                         minOccurrence: Int): Iterable[ContigSequence] = {","path":"src/main/scala/org/hammerlab/guacamole/commands/GermlineAssemblyCaller.scala","position":21,"original_position":21,"commit_id":"5de769bad14dcf9000f5c874dd00d3a98c7c94e1","original_commit_id":"1b6e0854d77bc50bd68639d007e0bb590d05204d","user":{"login":"ryan-williams","id":465045,"avatar_url":"https://avatars.githubusercontent.com/u/465045?v=3","gravatar_id":"","url":"https://api.github.com/users/ryan-williams","html_url":"https://github.com/ryan-williams","followers_url":"https://api.github.com/users/ryan-williams/followers","following_url":"https://api.github.com/users/ryan-williams/following{/other_user}","gists_url":"https://api.github.com/users/ryan-williams/gists{/gist_id}","starred_url":"https://api.github.com/users/ryan-williams/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ryan-williams/subscriptions","organizations_url":"https://api.github.com/users/ryan-williams/orgs","repos_url":"https://api.github.com/users/ryan-williams/repos","events_url":"https://api.github.com/users/ryan-williams/events{/privacy}","received_events_url":"https://api.github.com/users/ryan-williams/received_events","type":"User","site_admin":false},"body":"Now that `ContigSequence` is an alias for `IndexedSeq`, I am more in favor of having it (or an alias like it) here instead of `Array[Byte]`, as a way of enforcing that genomic sequences that we index in to are efficiently indexable.\r\n\r\nDo you want me to rename it to just `Sequence`? `GenomicSequence`? Something else? Leave it as `ContigSequence`?","created_at":"2016-04-01T15:04:39Z","updated_at":"2016-04-01T15:04:39Z","html_url":"https://github.com/hammerlab/guacamole/pull/417#discussion_r58218719","pull_request_url":"https://api.github.com/repos/hammerlab/guacamole/pulls/417","_links":{"self":{"href":"https://api.github.com/repos/hammerlab/guacamole/pulls/comments/58218719"},"html":{"href":"https://github.com/hammerlab/guacamole/pull/417#discussion_r58218719"},"pull_request":{"href":"https://api.github.com/repos/hammerlab/guacamole/pulls/417"}}},"pull_request":{"url":"https://api.github.com/repos/hammerlab/guacamole/pulls/417","id":64896347,"html_url":"https://github.com/hammerlab/guacamole/pull/417","diff_url":"https://github.com/hammerlab/guacamole/pull/417.diff","patch_url":"https://github.com/hammerlab/guacamole/pull/417.patch","issue_url":"https://api.github.com/repos/hammerlab/guacamole/issues/417","number":417,"state":"open","locked":false,"title":"decouple Reference sequences from Spark-broadcasts","user":{"login":"ryan-williams","id":465045,"avatar_url":"https://avatars.githubusercontent.com/u/465045?v=3","gravatar_id":"","url":"https://api.github.com/users/ryan-williams","html_url":"https://github.com/ryan-williams","followers_url":"https://api.github.com/users/ryan-williams/followers","following_url":"https://api.github.com/users/ryan-williams/following{/other_user}","gists_url":"https://api.github.com/users/ryan-williams/gists{/gist_id}","starred_url":"https://api.github.com/users/ryan-williams/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ryan-williams/subscriptions","organizations_url":"https://api.github.com/users/ryan-williams/orgs","repos_url":"https://api.github.com/users/ryan-williams/repos","events_url":"https://api.github.com/users/ryan-williams/events{/privacy}","received_events_url":"https://api.github.com/users/ryan-williams/received_events","type":"User","site_admin":false},"body":"only allowing instantiation of (and access to) References via Spark Broadcast objects was resulting in abstraction creep.\r\n\r\nlots of code touching Spark internals that didn't need to be, and lots of tests being heavier-weight spark tests.\r\n\r\nHere I've:\r\n- flattened `ContigSequence` into simply a type alias for `Array[Byte]`\r\n- replaced `ReferenceBroadcast` with `ReferenceGenome`; the latter just wraps a `Map[String, ContigSequence]`.\r\n- changed the {pileup,window}Flatmap* interfaces to take a reference and hide the broadcasting; the multipleRDDs version now takes a UDF that expects pileups and a reference.\r\n- pulled SparkContexts out of many tests and parts of the code that shouldn't have had one\n\n<!-- Reviewable:start -->\n---\nThis change is [<img src=\"https://reviewable.io/review_button.svg\" height=\"35\" align=\"absmiddle\" alt=\"Reviewable\"/>](https://reviewable.io/reviews/hammerlab/guacamole/417)\n<!-- Reviewable:end 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