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  1. IGB
  2. IGBF-3464

Deploy htsjdk-igb

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          Description

          Situation: In order to add CRAM file support (IGBF-1469) we need to update the HTSJDK dependency version. Currently we are using the artifact htsjdk-igb.

          Task: Investigate our use of the htsjdk-igb dependency. Determine how we can update this dependency.

          Github repo: https://github.com/lorainelab/htsjdk-igb

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              Issue Links

              blocks

              New Feature - A new feature of the product, which has yet to be developed. IGBF-3478 Add CRAM support to IGB

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-1469 Investigate supporting CRAM files

              • Major - Major loss of function.
              • Closed
              is blocked by

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3465 Update BigWig/BigBed htsjdk-igb version

              • Major - Major loss of function.
              • Closed
              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1418 Import htsjdk as OSGi bundle

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3484 Update htsjdk-igb to 3.0.0

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese added a comment -

                Tested on Mac using strategy described in one of my previous comments. Everything is working correctly, closing ticket.

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                nfreese Nowlan Freese added a comment - Tested on Mac using strategy described in one of my previous comments. Everything is working correctly, closing ticket.
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                ann.loraine Ann Loraine added a comment -

                PR is merged and IGB is built, with no errors.

                attn: Kaushik Gopu

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                ann.loraine Ann Loraine added a comment - PR is merged and IGB is built, with no errors. attn: Kaushik Gopu
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                kgopu Kaushik Gopu added a comment -
                • PR has been submitted.
                • It would be best to deploy bigWig (IGBF-3464) prior to merging this PR
                Show
                kgopu Kaushik Gopu added a comment - PR has been submitted. It would be best to deploy bigWig ( IGBF-3464 ) prior to merging this PR
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                nfreese Nowlan Freese added a comment -

                Commit looks good, ready for pull request.

                Note that it would be best to deploy the changes to Bigwig (see IGBF-3465) prior to merging this pull request.

                Show
                nfreese Nowlan Freese added a comment - Commit looks good, ready for pull request. Note that it would be best to deploy the changes to Bigwig (see IGBF-3465 ) prior to merging this pull request.
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                kgopu Kaushik Gopu added a comment - - edited

                Updated IGB's htsjdk and bigWig versions to 3.0.5 and 2.0.1, respectively in the IGB project pom.
                Changes are available to in this commit
                Moving to first level review

                Show
                kgopu Kaushik Gopu added a comment - - edited Updated IGB's htsjdk and bigWig versions to 3.0.5 and 2.0.1, respectively in the IGB project pom. Changes are available to in this commit Moving to first level review
                10 older comments

                  People

                  • Assignee:
                    kgopu Kaushik Gopu
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
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                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: