GitHub PullRequestReviewCommentEvent at 2014-07-19 15:12:40
Repository: schemas
Actor: dglazer
Payload: {"action":"created","comment":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/15144177","id":15144177,"diff_hunk":"@@ -1,139 +1,178 @@\n @namespace(\"org.ga4gh\")\n-protocol GAReads {\n \n-/*\n- * This file defines the objects used to represent a hierarchy of reads and alignments:\n- *    GAReadGroupSet >--< GAReadGroup --< fragment --< read --< alignment --< linear alignment\n- *\n+/**\n+ This file defines the objects used to represent a hierarchy of reads and alignments:\n+    GAReadGroupSet >--< GAReadGroup --< fragment --< read --< alignment --< linear alignment\n+ \n  * A GAReadGroupSet is a logical collection of GAReadGroup's.\n  * A GAReadGroup is all the data that’s processed the same way by the sequencer.\n- *    There are typically 1-10 GAReadGroup's in a GAReadGroupSet.\n- * A *fragment* is a single stretch of a DNA molecule.\n- *    There are typically millions of fragments in a GAReadGroup.\n- *    A fragment has a name (QNAME in BAM spec), a length (TLEN in BAM spec), and an array of reads.\n- * A *read* is a contiguous sequence of bases.\n- *    There are typically only one or two reads in a fragment. If there are two reads, they’re known as a mate pair.\n- *    A read has an array of base values, an array of base qualities, and alignment information.\n+   There are typically 1-10 GAReadGroup's in a GAReadGroupSet.\n+ * A *fragment* is a single stretch of a DNA molecule. There are typically\n+   millions of fragments in a GAReadGroup. A fragment has a name (QNAME in BAM\n+   spec), a length (TLEN in BAM spec), and an array of reads.\n+ * A *read* is a contiguous sequence of bases. There are typically only one or\n+   two reads in a fragment. If there are two reads, they’re known as a mate pair.\n+   A read has an array of base values, an array of base qualities, and alignment\n+   information.\n  * An *alignment* is the way alignment software maps a read to a reference.\n- *    There’s one primary alignment, and can be one or more secondary alignments.\n- *    Secondary alignments represent alternate possible mappings -- they are rarely reported by aligners.\n- * A *linear alignment* maps a string of bases to a reference using a single CIGAR string.\n- *    There’s one representative alignment, and can be one or more supplementary alignments.\n- *    Supplementary alignments represent chimeric reads -- they are rare.\n- *\n- * A GAReadAlignment object is a flattened representation of the bottom layers of this hierarchy.\n- *    There's exactly one such object per *linear alignment*.\n- *    The object contains alignment info, plus fragment and read info for easy access.\n+   There’s one primary alignment, and can be one or more secondary or","path":"src/main/resources/avro/reads.avdl","position":39,"original_position":39,"commit_id":"64dcd7f77b0ff270d7f816b563a3adb25f1d28f3","original_commit_id":"64dcd7f77b0ff270d7f816b563a3adb25f1d28f3","user":{"login":"dglazer","id":5824733,"avatar_url":"https://avatars.githubusercontent.com/u/5824733?","gravatar_id":"e57f933dd537b3774505904af0815af8","url":"https://api.github.com/users/dglazer","html_url":"https://github.com/dglazer","followers_url":"https://api.github.com/users/dglazer/followers","following_url":"https://api.github.com/users/dglazer/following{/other_user}","gists_url":"https://api.github.com/users/dglazer/gists{/gist_id}","starred_url":"https://api.github.com/users/dglazer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dglazer/subscriptions","organizations_url":"https://api.github.com/users/dglazer/orgs","repos_url":"https://api.github.com/users/dglazer/repos","events_url":"https://api.github.com/users/dglazer/events{/privacy}","received_events_url":"https://api.github.com/users/dglazer/received_events","type":"User","site_admin":false},"body":"Frank, I found this section clearer when secondary and supplementary were discussed separately, since my understanding is that they apply to different levels of the hierarchy:\r\n- secondary is what we call it when one read maps to more than one alignment\r\n- supplementary is what we call it when one alignment maps to more than one linear alignment\r\n(I don't love that terminology, but it is what's in use now.)\r\n\r\nAlso -- did you delete the \"they are rare\" comments intentionally? I found them useful in understanding the way these models work in practice, similar to how we give guidance above on the typical number of RGs per RGSet and the typical number of reads per RG. It's not normative, but it is helpful.","created_at":"2014-07-19T15:12:40Z","updated_at":"2014-07-19T15:12:40Z","html_url":"https://github.com/ga4gh/schemas/pull/100#discussion_r15144177","pull_request_url":"https://api.github.com/repos/ga4gh/schemas/pulls/100","_links":{"self":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/15144177"},"html":{"href":"https://github.com/ga4gh/schemas/pull/100#discussion_r15144177"},"pull_request":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/100"}}},"pull_request":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/100","id":18529185,"html_url":"https://github.com/ga4gh/schemas/pull/100","diff_url":"https://github.com/ga4gh/schemas/pull/100.diff","patch_url":"https://github.com/ga4gh/schemas/pull/100.patch","issue_url":"https://api.github.com/repos/ga4gh/schemas/issues/100","number":100,"state":"open","title":"Update alignment 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it can be merged in.\r\n\r\nThis provides more explicit definitions for the supplementary/secondary alignment flags, the cigar operators, and some of the alignment specific 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