Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.0.2 Minor Release
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Labels:
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Story Points:1
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Sprint:B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3
Description
We need to upgrade our sam/bam parsing library to be in line with the updated sam/bam specification. Currently some header flags which are part of the specification (i.e. SO) will cause exceptions to be thrown by the samtools libary and prevent the ability of users to load their data.
We should update our libary and parsers to resolve the issue.
Attachments
Issue Links
- relates to
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IGBF-1321 Test for errors due to htsjdk library update
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- Closed
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- Closed
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IGBF-1418 Import htsjdk as OSGi bundle
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- Closed
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- Closed
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | David Norris [ dcnorris ] | Kiran Korey [ kkorey ] |
| Sprint | B - Summer 2018 [ 48 ] |
| Story Points | 3 | 1 |
| Rank | Ranked lower |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018 [ 48 ] | B - Summer 2018, Summer 2018 Part 2 [ 48, 49 ] |
| Rank | Ranked higher |
| Fix Version/s | 9.0.2 [ 10600 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Summary | Sam File SO (Sorted Order) flag is not recognized by the version of samtools used by symloaders | Update BAM, tabix reader libraries |
| Assignee | Ivory Blakley [ ieclabau ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Assignee | Ivory Blakley [ ieclabau ] | Kiran Korey [ kkorey ] |
| Status | Reviewing [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Kiran Korey [ kkorey ] | Ivory Blakley [ ieclabau ] |
| Assignee | Ivory Blakley [ ieclabau ] | Kiran Korey [ kkorey ] |
| Status | Needs 1st Level Review [ 10005 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Assignee | Mason Meyer [ mason ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2 [ 48, 49 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3 [ 48, 49, 50 ] |
| Rank | Ranked higher |
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Mason Meyer [ mason ] | Kiran Korey [ kkorey ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | Open [ 1 ] |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3 [ 48, 49, 50 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1 [ 48, 49, 50, 51 ] |
| Labels | Advanced |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] | Kiran Korey [ kkorey ] |
| Status | Needs 1st Level Review [ 10005 ] | Open [ 1 ] |
| Status | Open [ 1 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] | Kiran Korey [ kkorey ] |
| Comment |
[ Does htsjdk have updated code replacing tribble-ext?
https://github.com/samtools/htsjdk/tree/master/src/main/java/htsjdk/tribble ] |
| Status | Reviewing [ 10301 ] | Open [ 1 ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1 [ 48, 49, 50, 51 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2 [ 48, 49, 50, 51, 52 ] |
| Rank | Ranked lower |
| Comment |
[ Thanks.
Looks like some module POMs list tribble-ext jar as a dependency but don't import any tribble packages. For example, java code in "bed" module does not appear to import any packages from tribble-ext, but the pom still mentions it as a dependency. Sorry to add more to this task: Please check each module that lists tribble-ext as a dependency and remove from the POM if no packages are imported. (There may be a tool that can automate this.) POMs mentioning tribble-ext: $ find . -name pom.xml | xargs grep tribble-ext ./core/das2/pom.xml: <artifactId>tribble-ext</artifactId> ./core/genometry/pom.xml: <artifactId>tribble-ext</artifactId> ./core/shared-lib-wrapper/pom.xml: <artifactId>tribble-ext</artifactId> ./plugins/bed/pom.xml: <artifactId>tribble-ext</artifactId> ./plugins/bam/pom.xml: <artifactId>tribble-ext</artifactId> ./plugins/BigBedHandler/pom.xml: <artifactId>tribble-ext</artifactId> ./plugins/BigWigHandler/pom.xml: <artifactId>tribble-ext</artifactId> ./developmentPlugins/TallyHandler/pom.xml: <artifactId>tribble-ext</artifactId> ./pom.xml: <artifactId>tribble-ext</artifactId> ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2 [ 48, 49, 50, 51, 52 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3 [ 48, 49, 50, 51, 52, 53 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Resolution | Done [ 10000 ] | |
| Status | In Progress [ 3 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 16983 ] | Fall 2019 Workflow Update [ 19765 ] |
| Workflow | Fall 2019 Workflow Update [ 19765 ] | Revised Fall 2019 Workflow Update [ 21884 ] |