{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1104","repository_url":"https://api.github.com/repos/bigdatagenomics/adam","labels_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1104/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1104/comments","events_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1104/events","html_url":"https://github.com/bigdatagenomics/adam/pull/1104","id":170017632,"number":1104,"title":"Resolves various single file save/header issues","user":{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars.githubusercontent.com/u/3752466?v=3","gravatar_id":"","url":"https://api.github.com/users/fnothaft","html_url":"https://github.com/fnothaft","followers_url":"https://api.github.com/users/fnothaft/followers","following_url":"https://api.github.com/users/fnothaft/following{/other_user}","gists_url":"https://api.github.com/users/fnothaft/gists{/gist_id}","starred_url":"https://api.github.com/users/fnothaft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnothaft/subscriptions","organizations_url":"https://api.github.com/users/fnothaft/orgs","repos_url":"https://api.github.com/users/fnothaft/repos","events_url":"https://api.github.com/users/fnothaft/events{/privacy}","received_events_url":"https://api.github.com/users/fnothaft/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2016-08-08T20:29:23Z","updated_at":"2016-08-19T17:11:15Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/1104","html_url":"https://github.com/bigdatagenomics/adam/pull/1104","diff_url":"https://github.com/bigdatagenomics/adam/pull/1104.diff","patch_url":"https://github.com/bigdatagenomics/adam/pull/1104.patch"},"body":"Resolves #1009, #1059, #1058, #676."},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/comments/241076869","html_url":"https://github.com/bigdatagenomics/adam/pull/1104#issuecomment-241076869","issue_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1104","id":241076869,"user":{"login":"jpdna","id":7423296,"avatar_url":"https://avatars.githubusercontent.com/u/7423296?v=3","gravatar_id":"","url":"https://api.github.com/users/jpdna","html_url":"https://github.com/jpdna","followers_url":"https://api.github.com/users/jpdna/followers","following_url":"https://api.github.com/users/jpdna/following{/other_user}","gists_url":"https://api.github.com/users/jpdna/gists{/gist_id}","starred_url":"https://api.github.com/users/jpdna/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jpdna/subscriptions","organizations_url":"https://api.github.com/users/jpdna/orgs","repos_url":"https://api.github.com/users/jpdna/repos","events_url":"https://api.github.com/users/jpdna/events{/privacy}","received_events_url":"https://api.github.com/users/jpdna/received_events","type":"User","site_admin":false},"created_at":"2016-08-19T17:11:15Z","updated_at":"2016-08-19T17:11:15Z","body":"Trying to output a `-single` sam file (rather than bam) works fine as:\r\n```adam-submit transform testb.adam testb.rountrip.sam -single```\r\nand samtools is then happy to operate on that sam file, including converting it to bam.\r\n\r\nAlso - I did same test and got same result of samtools not being to read the round tripped bam when using the `unsorted.bam` file we use in our unit tests.\r\n\r\n```\r\nadam-submit transform unsorted.sam unsorted.adam\r\n../adam/bin/adam-submit transform unsorted.adam unsorted.roundtrip.bam -single\r\n\r\n \r\nsamtools flagstat unsorted.roundtrip.bam\r\n0 + 0 in total (QC-passed reads + QC-failed reads)\r\n0 + 0 secondary\r\n0 + 0 supplementary\r\n0 + 0 duplicates\r\n0 + 0 mapped (N/A : N/A)\r\n0 + 0 paired in sequencing\r\n0 + 0 read1\r\n0 + 0 read2\r\n0 + 0 properly paired (N/A : N/A)\r\n0 + 0 with itself and mate mapped\r\n0 + 0 singletons (N/A : N/A)\r\n0 + 0 with mate mapped to a different chr\r\n0 + 0 with mate mapped to a different chr (mapQ>=5)\r\n```\r\n"}}
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