Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Blocker
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.1.0 Major Release
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Labels:
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Story Points:2
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Epic Link:
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Sprint:Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov
Description
Working with PacBio long reads from a URL, hit a SocketTimeoutException. The reads do not display correctly - appearing as unfilled squares. The read scores also seem to be incorrect, though that may be a separate issue.
Example bam can be found here
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Winter 2018 Sprint 3 [ 58 ] | |
| Labels | Intermediate |
| Rank | Ranked higher |
| Sprint | Winter 2018 Sprint 3 [ 58 ] | Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 58, 59 ] |
| Labels | Intermediate | Advanced |
| Sprint | Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 58, 59 ] | Winter 2018 Sprint 3 [ 58 ] |
| Rank | Ranked lower |
| Sprint | Winter 2018 Sprint 3 [ 58 ] | Winter 2018 Sprint 3, Spring 2019 Sprint 2 [ 58, 60 ] |
| Rank | Ranked higher |
| Sprint | Winter 2018 Sprint 3, Spring 2019 Sprint 2 [ 58, 60 ] | Winter 2018 Sprint 3 [ 58 ] |
| Rank | Ranked lower |
| Comment | [ Note: Requires understanding the format and alignments. ] |
| Epic Link | IGBF-1765 [ 17855 ] |
| Fix Version/s | 9.1.0 Major Release [ 10601 ] | |
| Sprint | Winter 2018 Sprint 3 [ 58 ] | Winter 2018 Sprint 3, Summer 2019 Sprint 11 [ 58, 70 ] |
| Sprint | Winter 2018 Sprint 3, Summer 2019 Sprint 11 [ 58, 70 ] | Winter 2018 Sprint 3, Summer 2019 Sprint 10 [ 58, 69 ] |
| Sprint | Winter 2018 Sprint 3, Summer 2019 Sprint 10 [ 58, 69 ] | Winter 2018 Sprint 3, Summer 2019 Sprint 11 [ 58, 70 ] |
| Sprint | Winter 2018 Sprint 3, Summer 2019 Sprint 11 [ 58, 70 ] | Winter 2018 Sprint 3, Summer 2019 Sprint 12 [ 58, 71 ] |
| Sprint | Winter 2018 Sprint 3, Summer 2019 Sprint 12 [ 58, 71 ] | Winter 2018 Sprint 3, Summer 2019 Sprint 13 [ 58, 72 ] |
| Workflow | Loraine Lab Workflow [ 18182 ] | Fall 2019 Workflow Update [ 18924 ] |
| Sprint | Winter 2018 Sprint 3, Fall 2019 Sprint 1 [ 58, 72 ] | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2 [ 58, 72, 73 ] |
| Rank | Ranked higher |
| Sprint | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2 [ 58, 72, 73 ] | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 4 [ 58, 72, 73, 74 ] |
| Rank | Ranked higher |
| Status | Open [ 1 ] | To-Do [ 10305 ] |
| Priority | Minor [ 4 ] | Blocker [ 1 ] |
| Summary | PacBio reads not showing correctly | Investigate: PacBio reads not showing correctly |
| Rank | Ranked lower |
| Sprint | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3 [ 58, 72, 73, 74 ] | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 4 [ 58, 72, 73, 75 ] |
| Rank | Ranked lower |
| Sprint | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct [ 58, 72, 73, 75 ] | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 58, 72, 73, 75, 76 ] |
| Rank | Ranked higher |
| Workflow | Fall 2019 Workflow Update [ 18924 ] | Revised Fall 2019 Workflow Update [ 21167 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | pacBio.bam [ 14453 ] | |
| Attachment | pacBio.bam.bai [ 14454 ] |
| Fix Version/s | 9.1.0 Major Release [ 10601 ] |
| Attachment | 1 (1).txt [ 14455 ] |
| Attachment | igb.png [ 14457 ] | |
| Attachment | pacBio-OneRead_5224S42EQUALS.bam [ 14458 ] | |
| Attachment | pacBio-OneRead_5224S42EQUALS.bam.bai [ 14459 ] | |
| Attachment | pacBio-OneRead_5224S42M.bam [ 14460 ] | |
| Attachment | pacBio-OneRead_5224S42M.bam.bai [ 14461 ] | |
| Attachment | pacBio-OneRead.bam [ 14462 ] | |
| Attachment | pacBio-OneRead.bam.bai [ 14463 ] |
| Attachment | pacBio-OneRead_42EQUALS.bam [ 14464 ] | |
| Attachment | pacBio-OneRead_42EQUALS.bam.bai [ 14465 ] | |
| Attachment | pacBio-OneRead_42X.bam [ 14466 ] | |
| Attachment | pacBio-OneRead_42X.bam.bai [ 14467 ] |
| Fix Version/s | 9.1.0 Major Release [ 10601 ] |
| Sprint | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 58, 72, 73, 75, 76 ] | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov [ 58, 72, 73, 75, 76, 77 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Nowlan Freese [ nfreese ] | Noor Zahara [ noor91zahara ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Nowlan Freese [ nfreese ] | Noor Zahara [ noor91zahara ] |
| Summary | Investigate: PacBio reads not showing correctly | Implement better handling of CIGAR string in BAM/SAM |