{"action":"created","comment":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/comments/29078531","id":29078531,"diff_hunk":"@@ -346,6 +347,7 @@ public void addPair(final String name, final int contig, final int start1, final\n         end2.setAlignmentStart(start2);\n         end2.setReadNegativeStrandFlag(true);\n         end2.setCigarString(readLength + \"M\");\n+        end2.setAttribute(ReservedTagConstants.NM,0);","path":"src/java/htsjdk/samtools/SAMRecordSetBuilder.java","position":null,"original_position":12,"commit_id":"9fa206ba2b05bb59c2b6a9483bf504e04760d19f","original_commit_id":"611511827d3a89a81e2c4d0f145780c49ef3330c","user":{"login":"yfarjoun","id":2745554,"avatar_url":"https://avatars.githubusercontent.com/u/2745554?v=3","gravatar_id":"","url":"https://api.github.com/users/yfarjoun","html_url":"https://github.com/yfarjoun","followers_url":"https://api.github.com/users/yfarjoun/followers","following_url":"https://api.github.com/users/yfarjoun/following{/other_user}","gists_url":"https://api.github.com/users/yfarjoun/gists{/gist_id}","starred_url":"https://api.github.com/users/yfarjoun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yfarjoun/subscriptions","organizations_url":"https://api.github.com/users/yfarjoun/orgs","repos_url":"https://api.github.com/users/yfarjoun/repos","events_url":"https://api.github.com/users/yfarjoun/events{/privacy}","received_events_url":"https://api.github.com/users/yfarjoun/received_events","type":"User","site_admin":false},"body":"OK. fixed it. look again?\n\nOn Fri, Apr 24, 2015 at 2:56 PM, Yossi Farjoun <farjoun@broadinstitute.org>\nwrote:\n\n> impossible. :-/\n>\n> On Fri, Apr 24, 2015 at 2:13 PM, Nils Homer <notifications@github.com>\n> wrote:\n>\n>> In src/java/htsjdk/samtools/SAMRecordSetBuilder.java\n>> <https://github.com/samtools/htsjdk/pull/223#discussion_r29072067>:\n>>\n>> > @@ -346,6 +347,7 @@ public void addPair(final String name, final int contig, final int start1, final\n>> >          end2.setAlignmentStart(start2);\n>> >          end2.setReadNegativeStrandFlag(true);\n>> >          end2.setCigarString(readLength + \"M\");\n>> > +        end2.setAttribute(ReservedTagConstants.NM,0);\n>>\n>> I don't think this is the only place where NM is not set (see the other\n>> addPair methods). Do you want to add it to createReadNoFlag?\n>>\n>> —\n>> Reply to this email directly or view it on GitHub\n>> <https://github.com/samtools/htsjdk/pull/223/files#r29072067>.\n>>\n>\n>\n","created_at":"2015-04-24T19:31:59Z","updated_at":"2015-04-24T19:31:59Z","html_url":"https://github.com/samtools/htsjdk/pull/223#discussion_r29078531","pull_request_url":"https://api.github.com/repos/samtools/htsjdk/pulls/223","_links":{"self":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/comments/29078531"},"html":{"href":"https://github.com/samtools/htsjdk/pull/223#discussion_r29078531"},"pull_request":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/223"}}},"pull_request":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/223","id":34062232,"html_url":"https://github.com/samtools/htsjdk/pull/223","diff_url":"https://github.com/samtools/htsjdk/pull/223.diff","patch_url":"https://github.com/samtools/htsjdk/pull/223.patch","issue_url":"https://api.github.com/repos/samtools/htsjdk/issues/223","number":223,"state":"open","locked":false,"title":"Yf geometrical 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