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  1. Bug Repository
  2. BUG-310

handle tabix files

          Details

          • Type: Task
          • Status: Closed (View Workflow)
          • Priority: Minor
          • Resolution: Fixed
          • Labels:
            None

            Description

            Add the ability to process tabix files

              Attachments

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-622 File format issues

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

                  Activity

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                  lfrohman Lance Frohman (Inactive) created issue -
                  lfrohman Lance Frohman (Inactive) made changes -
                  Field Original Value New Value
                  Status Open [ 1 ] Resolved [ 5 ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  Assignee Lance Frohman [ lfrohman ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project Genentech [ 10034 ] Bug Repository [ 10030 ]
                  Key TODO-4 BUG-310
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Fuquan Wang [ fwang4 ]
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                  fwang4 Fuquan Wang (Inactive) added a comment -

                  *tabix file not supported in 7.0.0 (11884) Mac.

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                  fwang4 Fuquan Wang (Inactive) added a comment - *tabix file not supported in 7.0.0 (11884) Mac.
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Assignee Fuquan Wang [ fwang4 ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Could you test this out on windows?

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Could you test this out on windows?
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Katharine Kubiak [ kkubiak ]
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Can you attach a tabix file to this issue?

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Can you attach a tabix file to this issue?
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Attachment CpG Islands.bed.gz [ 11095 ]
                  Attachment CpG Islands.bed.gz.tbi [ 11096 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-622 [ BUG-622 ]
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                  richard Richard Linchangco (Inactive) added a comment - - edited

                  Passed V.13624, Mac, Java 1.06.0_37

                  Tested with tabix files from:

                  http://bioviz.org/filerepo/CpG Islands.bed.gz
                  http://bioviz.org/filerepo/CpG Islands.bed.gz.tbi

                  Search within first 60,000 bases (otherwise files is empty)

                  Integration of tabix file support in IGB 7.0.0(13624) could label this as a LEGACY bug

                  Show
                  richard Richard Linchangco (Inactive) added a comment - - edited Passed V.13624, Mac, Java 1.06.0_37 Tested with tabix files from: http://bioviz.org/filerepo/CpG Islands.bed.gz http://bioviz.org/filerepo/CpG Islands.bed.gz.tbi Search within first 60,000 bases (otherwise files is empty) Integration of tabix file support in IGB 7.0.0(13624) could label this as a LEGACY bug
                  richard Richard Linchangco (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Reporter Lance Frohman [ lfrohman ] Alyssa Gulledge [ alyssa ]
                  Description Add the ability to process tabix files - this will be done as a separate bundle if possible. Add the ability to process tabix files
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Still need to ensure that this file format is readable.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Still need to ensure that this file format is readable.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      alyssa Alyssa Gulledge (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: