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  1. IGB
  2. IGBF-1469

Investigate supporting CRAM files

        Details

        • Story Points:
          3
        • Epic Link:
        • Sprint:
          Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2 2023 Sep 17, Fall 4 2023 Oct 16

          Description

          Discussion on twitter:

          https://twitter.com/pjacock/status/500208907651153920

          CRAM is a compressed, random-access file format used instead of BAM. It may be better. Not yet widely used but may be in future. Supporting CRAM could benefit users.

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              Issue Links

              is blocked by

              Task - A task that needs to be done. IGBF-3464 Deploy htsjdk-igb

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-165 [ 14687 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
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                mason Mason Meyer (Inactive) made changes -
                Epic Link IGBF-165 [ 14687 ] IGBF-440 [ 15498 ]
                mason Mason Meyer (Inactive) made changes -
                Rank Ranked lower
                mason Mason Meyer (Inactive) made changes -
                Epic Link IGBF-440 [ 15498 ] IGBF-501 [ 15563 ]
                mason Mason Meyer (Inactive) made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Project IGB [ 10840 ] Deep Backlog [ 11041 ]
                Key IGBF-166 DB-174
                Workflow Loraine Lab Workflow [ 14817 ] jira [ 16881 ]
                nfreese Nowlan Freese made changes -
                Assignee David Norris [ dcnorris ]
                nfreese Nowlan Freese made changes -
                Project Deep Backlog [ 11041 ] IGB [ 10840 ]
                Key DB-174 IGBF-1469
                Workflow jira [ 16881 ] Loraine Lab Workflow [ 18183 ]
                nfreese Nowlan Freese made changes -
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                ann.loraine Ann Loraine made changes -
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                nfreese Nowlan Freese made changes -
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                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Story Points 1
                Sprint Winter 2018 Sprint 3 [ 58 ]
                Labels Advanced
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3 [ 58 ] Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 58, 59 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 58, 59 ] Winter 2018 Sprint 3 [ 58 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3 [ 58 ] Winter 2018 Sprint 3, Spring 2019 Sprint 2 [ 58, 60 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Spring 2019 Sprint 2 [ 58, 60 ] Winter 2018 Sprint 3 [ 58 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked lower
                ann.loraine Ann Loraine made changes -
                Fix Version/s 9.1.0 Major Release [ 10601 ]
                Story Points 1 2
                Sprint Winter 2018 Sprint 3 [ 58 ] Winter 2018 Sprint 3, Spring 2019 Sprint 6 [ 58, 64 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Spring 2019 Sprint 6 [ 58, 64 ] Winter 2018 Sprint 3, Spring 2019 Sprint 7 [ 58, 66 ]
                ann.loraine Ann Loraine made changes -
                Story Points 2 3.5
                ann.loraine Ann Loraine made changes -
                Comment [ BAM files are too big :-) ]
                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Spring 2019 Sprint 7 [ 58, 66 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8 [ 58, 67 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-501 [ 15563 ] IGBF-1765 [ 17855 ]
                ann.loraine Ann Loraine made changes -
                Story Points 3.5 2
                ann.loraine Ann Loraine made changes -
                Story Points 2 3
                ann.loraine Ann Loraine made changes -
                Story Points 3 2
                shamika Shamika Gajanan Kulkarni (Inactive) made changes -
                Assignee Shamika Gajanan Kulkarni [ shamika ]
                shamika Shamika Gajanan Kulkarni (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                shamika Shamika Gajanan Kulkarni (Inactive) made changes -
                Status In Progress [ 3 ] Open [ 1 ]
                shamika Shamika Gajanan Kulkarni (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8 [ 58, 67 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 9 [ 58, 67, 68 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 9 [ 58, 67, 68 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 11 [ 58, 67, 70 ]
                Assignee Shamika Gajanan Kulkarni [ shamika ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 11 [ 58, 67, 70 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 12 [ 58, 67, 71 ]
                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 12 [ 58, 67, 71 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 13 [ 58, 67, 72 ]
                ann.loraine Ann Loraine made changes -
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                noor91zahara Noor Zahara (Inactive) made changes -
                Rank Ranked higher
                noor91zahara Noor Zahara (Inactive) made changes -
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                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 13 [ 58, 67, 72 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 14 [ 58, 67, 73 ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18183 ] Fall 2019 Workflow Update [ 18723 ]
                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2019 Sprint 2 [ 58, 67, 73 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2019 Sprint 6 [ 58, 67, 76 ]
                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2019 Sprint 5 [ 58, 67, 76 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2019 Sprint 4 [ 58, 67, 75 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 4 : 30 Sep to 11 Oct [ 58, 67, 75 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 9 : 9 Dec to 20 Dec [ 58, 67, 80 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 18723 ] Revised Fall 2019 Workflow Update [ 20845 ]
                Status Open [ 1 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Fix Version/s 9.1.0 Major Release [ 10601 ]
                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 9 : 9 Dec to 20 Dec [ 58, 67, 80 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8 [ 58, 67 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
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                nfreese Nowlan Freese made changes -
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                nfreese Nowlan Freese made changes -
                Story Points 2 3
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8 [ 58, 67 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2 2023 Sep 17 [ 58, 67, 178 ]
                Assignee Kaushik Gopu [ kgopu ]
                nfreese Nowlan Freese made changes -
                Attachment A_thaliana_Jun_2009_Chr1.bam [ 17963 ]
                Attachment A_thaliana_Jun_2009_Chr1.bam.bai [ 17964 ]
                Attachment A_thaliana_Jun_2009_Chr1.cram [ 17965 ]
                Attachment A_thaliana_Jun_2009_Chr1.sam [ 17966 ]
                nfreese Nowlan Freese made changes -
                Attachment A_thaliana_Jun_2009_Chr1.cram.crai [ 17967 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2 2023 Sep 17 [ 58, 67, 178 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2 2023 Sep 17, Fall 3 2023 Oct 2 [ 58, 67, 178, 179 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Link This issue is blocked by IGBF-3464 [ IGBF-3464 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Sprint Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2 2023 Sep 17, Fall 3 2023 Oct 2 [ 58, 67, 178, 179 ] Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2 2023 Sep 17, Fall 4 [ 58, 67, 178, 180 ]
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1765 [ 17855 ] IGBF-3467 [ 22628 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 10.0.0 Major Release [ 10900 ]

                  People

                  • Assignee:
                    kgopu Kaushik Gopu
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: