Details
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Type: Bug
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Status: Closed (View Workflow)
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Priority: Minor
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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:None
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Story Points:2
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Sprint:Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3, Spring 2019 Sprint 1
Description
Depth graph track operations are used to add up the amount of read depth from bam/sam files. The soft-clipped portion of a read should not count towards either Depth Graph (Start) or Depth Graph (All).
Currently Depth Graph (All) does not include the soft-clipped portion (correct). However, Depth Graph (Start) does count the soft-clipped portion (bug).
Example soft-clip files can be found in Dropbox > IGB > Jira Issues > IGBF-1291 Soft-Clip > exampleFiles
Potential classes worth investigating:
SeqSymSummarizer > getSpanStartSummary
Delegate - getRegion
Attachments
Issue Links
- relates to
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IGBF-1291 Show soft-clipped bases in BAM files
- Closed
Activity
Nowlan Freese
created issue -
Nowlan Freese
made changes -
Nowlan Freese
made changes -
Nowlan Freese
made changes -
Nowlan Freese
made changes -
Attachment | softClipShifted2.sam [ 14173 ] |
Nowlan Freese
made changes -
Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
Nowlan Freese
made changes -
Status | Open [ 1 ] | In Progress [ 3 ] |
Nowlan Freese
made changes -
Attachment | onlyMatchesNegativeShifted.sam [ 14177 ] | |
Attachment | onlyMatchesShifted-2.sam [ 14178 ] |
Pranav Sanjay Tambvekar (Inactive)
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Pranav Sanjay Tambvekar (Inactive)
made changes -
Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
Nowlan Freese
made changes -
Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
Nowlan Freese
made changes -
Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
Pranav Sanjay Tambvekar (Inactive)
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Nowlan Freese
made changes -
Status | Pull Request Submitted [ 10101 ] | Reviewing [ 10301 ] |
Nowlan Freese
made changes -
Attachment | example.bed [ 14182 ] | |
Attachment | soft-match-deletion-match-insertion-match-soft.sam [ 14183 ] |
Nowlan Freese
made changes -
Attachment | VCF_HomoSapien_EDITED.vcf [ 14184 ] |
Pranav Sanjay Tambvekar (Inactive)
made changes -
Status | Reviewing [ 10301 ] | Needs 1st Level Review [ 10005 ] |
Pranav Sanjay Tambvekar (Inactive)
made changes -
Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
Nowlan Freese
made changes -
Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] | Pranav Sanjay Tambvekar [ ptambvek ] |
Pranav Sanjay Tambvekar (Inactive)
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Nowlan Freese
made changes -
Status | Pull Request Submitted [ 10101 ] | Reviewing [ 10301 ] |
Nowlan Freese
made changes -
Attachment | GFF3_example_1_EDITED.gff3 [ 14185 ] |
Nowlan Freese
made changes -
Attachment | GFF3_example_1_EDITED_negative.gff3 [ 14186 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Fall 2018 Sprint 4 [ 54 ] | Fall 2018 Sprint 4, Fall 2018 Sprint 5 [ 54, 55 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Fix Version/s | 9.1.0 Major Release [ 10601 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Fall 2018 Sprint 4, Fall 2018 Sprint 5 [ 54, 55 ] | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1 [ 54, 55, 56 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Status | Reviewing [ 10301 ] | Needs Testing [ 10002 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1 [ 54, 55, 56 ] | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2 [ 54, 55, 56, 57 ] |
Ann Loraine
made changes -
Assignee | Pranav Sanjay Tambvekar [ ptambvek ] | Srishtee Marotkar [ srishtee ] |
Srishtee Marotkar (Inactive)
made changes -
Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
Srishtee Marotkar (Inactive)
made changes -
Attachment | IGBF1441_Testing.docx [ 14202 ] |
Srishtee Marotkar (Inactive)
made changes -
Comment | [ Details for Failed Test Cases ] |
Srishtee Marotkar (Inactive)
made changes -
Status | Testing In Progress [ 10003 ] | Open [ 1 ] |
Srishtee Marotkar (Inactive)
made changes -
Assignee | Srishtee Marotkar [ srishtee ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2 [ 54, 55, 56, 57 ] | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3 [ 54, 55, 56, 57, 58 ] |
Nowlan Freese
made changes -
Status | Open [ 1 ] | In Progress [ 3 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Assignee | Srishtee Marotkar [ srishteem ] |
Srishtee Marotkar (Inactive)
made changes -
Attachment | IGBF1441_Review_Screenshot.PNG [ 14204 ] |
Srishtee Marotkar (Inactive)
made changes -
Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
Srishtee Marotkar (Inactive)
made changes -
Assignee | Srishtee Marotkar [ srishteem ] | Nowlan Freese [ nfreese ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3 [ 54, 55, 56, 57, 58 ] | Fall 2018 Sprint 4, Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 54, 55, 56, 57, 58, 59 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] | Kiran Korey [ kkorey ] |
Nowlan Freese
made changes -
Assignee | Kiran Korey [ kkorey ] | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Nowlan Freese
made changes -
Attachment | softClip-DepthGraphStart-CORRECT.png [ 14241 ] |
Ann Loraine
made changes -
Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
made changes -
Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Status | Reviewing Pull Request [ 10303 ] | Needs Testing [ 10002 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Resolution | Done [ 10000 ] | |
Status | Needs Testing [ 10002 ] | Closed [ 6 ] |
Nowlan Freese
made changes -
Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Assignee | Pranav Sanjay Tambvekar [ ptambvek ] | Srishtee Marotkar [ srishteem ] |
Ann Loraine
made changes -
Workflow | Loraine Lab Workflow [ 18147 ] | Fall 2019 Workflow Update [ 19967 ] |
Ann Loraine
made changes -
Workflow | Fall 2019 Workflow Update [ 19967 ] | Revised Fall 2019 Workflow Update [ 22088 ] |
Nowlan Freese
made changes -
Assignee | Srishtee Marotkar [ srishteem ] | Nowlan Freese [ nfreese ] |