{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1963","repository_url":"https://api.github.com/repos/galaxyproject/tools-iuc","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1963/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1963/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1963/events","html_url":"https://github.com/galaxyproject/tools-iuc/pull/1963","id":338320898,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk5Mjg0MDk4","number":1963,"title":"samtools view update to v1.7","user":{"login":"bernt-matthias","id":25689525,"node_id":"MDQ6VXNlcjI1Njg5NTI1","avatar_url":"https://avatars1.githubusercontent.com/u/25689525?v=4","gravatar_id":"","url":"https://api.github.com/users/bernt-matthias","html_url":"https://github.com/bernt-matthias","followers_url":"https://api.github.com/users/bernt-matthias/followers","following_url":"https://api.github.com/users/bernt-matthias/following{/other_user}","gists_url":"https://api.github.com/users/bernt-matthias/gists{/gist_id}","starred_url":"https://api.github.com/users/bernt-matthias/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bernt-matthias/subscriptions","organizations_url":"https://api.github.com/users/bernt-matthias/orgs","repos_url":"https://api.github.com/users/bernt-matthias/repos","events_url":"https://api.github.com/users/bernt-matthias/events{/privacy}","received_events_url":"https://api.github.com/users/bernt-matthias/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-07-04T15:42:29Z","updated_at":"2018-07-09T22:50:57Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1963","html_url":"https://github.com/galaxyproject/tools-iuc/pull/1963","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/1963.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/1963.patch"},"body":"This updates samtools view to v1.7\r\n\r\nDiscussion:\r\n\r\n- [ ] Do we need samtools view based tools: slice_bam, bam_to_cram, bam_to_sam, cram_to_bam, and sam_to_bam. The logic with reference data and indices could potentially integrated into samtools_view.\r\n  - Note that I would have also the updated tools which I could push here, but lets decide first\r\n- [ ] tool version is now 2.xx can we change it to 1.7+galaxy2.xx?\r\n- [ ] macro PREPIDX\r\n  - [ ] for cram there was a test for the presence of the index, do we need this also for bam\r\n  - [ ] do we want indexing for SAM files? then tabix is needed which seems out-of-date in bioconda (0.2.5 available, latest 1.8 in htslib\r\n- [ ] do we need to allow explicitely for the different BAM data types, I guess we need them all.\r\n- [ ] check logic of setting outtype. also if statements for other types necessary? Can we simplify this?\r\n- [ ] readtags as repeat or text field\r\n- [ ] input of reference fasta: allow fai? planemo complains about fasta.gz\r\n- [ ] output sam: dbkey action needed? change_format needs to be replaced or improved\r\nchange_format deprecated?\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments/403644525","html_url":"https://github.com/galaxyproject/tools-iuc/pull/1963#issuecomment-403644525","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1963","id":403644525,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMzY0NDUyNQ==","user":{"login":"bernt-matthias","id":25689525,"node_id":"MDQ6VXNlcjI1Njg5NTI1","avatar_url":"https://avatars1.githubusercontent.com/u/25689525?v=4","gravatar_id":"","url":"https://api.github.com/users/bernt-matthias","html_url":"https://github.com/bernt-matthias","followers_url":"https://api.github.com/users/bernt-matthias/followers","following_url":"https://api.github.com/users/bernt-matthias/following{/other_user}","gists_url":"https://api.github.com/users/bernt-matthias/gists{/gist_id}","starred_url":"https://api.github.com/users/bernt-matthias/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bernt-matthias/subscriptions","organizations_url":"https://api.github.com/users/bernt-matthias/orgs","repos_url":"https://api.github.com/users/bernt-matthias/repos","events_url":"https://api.github.com/users/bernt-matthias/events{/privacy}","received_events_url":"https://api.github.com/users/bernt-matthias/received_events","type":"User","site_admin":false},"created_at":"2018-07-09T22:50:57Z","updated_at":"2018-07-09T22:50:57Z","author_association":"CONTRIBUTOR","body":"> I think we should keep the format conversion tools (sam <-> bam <-> cram) for usability/dicoverability reasons. Slice could be eliminated.\r\n\r\nAgreed. What would be the IUC way to remove slice? Delete it? Or mark it deprecated..? How?\r\n\r\n>     New version scheme seems good to me, assuming that we detect 1.7+g is > 2.x\r\n\r\nJep. Can someone answer if this works? Otherwise I would suggest to increase the version slowly, such that samtools version will catch up eventually. \r\n\r\n>    I don't know about cram indexes, but I think we can assume in galaxy that all files of type \"bam\" are indexed. I say no indexing for sam files\r\n\r\nOK. \r\n\r\n>     Would be nice to add the other galaxy bam input types(that are not indexed) for tools like view that don't need an index:\r\n>         qname_input_sorted.bam\r\n>         qname_sorted.bam\r\n>         unsorted.bam\r\n\r\nOK. Do we need to add them explicitely? Or are they implicitely allowed anyway, because of the data types class structure?\r\n\r\n>     I think the tool should ask about output type (.e.g. bam, sam, cram, indexed bam(implies coord sorting), indexed cram) and remove the \"same\" type - which, IMHO, adds complexity without much benefit. It would be tough to render a workflow from a tool using a same type. (left an inline comment to this effect)\r\n\r\nOK\r\n\r\n>     Read tags support looks fine to me as a repeat\r\n\r\nOK\r\n\r\n>     I think it's reasonable to require an fa even if the tool only really needs the index. fasta.gz should be supported\r\n\r\nI will check\r\n\r\n    Sorry - I don't know about the change_format bits - maybe someone else will\r\n"}}
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