[IGBF-1441] Fix Depth Graph (Start) Soft-clip coordinates - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Minor
Resolution: Done
Affects Version/s: None
Fix Version/s: 9.1.0 Major Release
Labels:
None

Story Points:
2
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

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Attachments

example.bed
0.1 kB
29/Oct/18 1:22 PM
GFF3_example_1_EDITED_negative.gff3
0.8 kB
31/Oct/18 12:21 PM
GFF3_example_1_EDITED.gff3
0.8 kB
31/Oct/18 12:16 PM
IGBF1441_Review_Screenshot.PNG
205 kB
10/Jan/19 2:00 PM
IGBF1441_Testing.docx
603 kB
18/Dec/18 5:55 PM
onlyMatchesNegativeShifted.sam
0.1 kB
24/Oct/18 2:56 PM
onlyMatchesShifted-2.sam
0.2 kB
24/Oct/18 2:56 PM
softClip-depthGraphStart.png
79 kB
24/Oct/18 10:11 AM
softClip-DepthGraphStart-CORRECT.png
109 kB
05/Feb/19 4:56 PM
softClipShifted2.sam
0.2 kB
24/Oct/18 12:25 PM
soft-match-deletion-match-insertion-match-soft.sam
0.1 kB
29/Oct/18 1:22 PM
VCF_HomoSapien_EDITED.vcf
1 kB
30/Oct/18 10:45 AM

Issue Links

relates to

IGBF-1291 Show soft-clipped bases in BAM files

Closed

Activity

Ascending order - Click to sort in descending order

Nowlan Freese created issue - 24/Oct/18 10:11 AM

Nowlan Freese made changes - 24/Oct/18 10:11 AM

Field	Original Value	New Value
Link		This issue blocks ~~IGBF-1291~~ [ ~~IGBF-1291~~ ]

Nowlan Freese made changes - 24/Oct/18 10:32 AM

Link

This issue relates to ~~IGBF-1291~~ [ ~~IGBF-1291~~ ]

Nowlan Freese made changes - 24/Oct/18 10:33 AM

Link

This issue blocks ~~IGBF-1291~~ [ ~~IGBF-1291~~ ]

Nowlan Freese made changes - 24/Oct/18 12:25 PM

Attachment

softClipShifted2.sam [ 14173 ]

Nowlan Freese made changes - 24/Oct/18 12:26 PM

Assignee

Pranav Sanjay Tambvekar [ ptambvek ]

Nowlan Freese made changes - 24/Oct/18 12:26 PM

Status

Open [ 1 ]

In Progress [ 3 ]

Nowlan Freese made changes - 24/Oct/18 2:56 PM

Attachment		onlyMatchesNegativeShifted.sam [ 14177 ]
Attachment		onlyMatchesShifted-2.sam [ 14178 ]

Pranav Sanjay Tambvekar (Inactive) made changes - 25/Oct/18 3:51 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Pranav Sanjay Tambvekar (Inactive) made changes - 25/Oct/18 3:52 PM

Assignee

Pranav Sanjay Tambvekar [ ptambvek ]

Nowlan Freese made changes - 25/Oct/18 4:35 PM

Status

Needs 1st Level Review [ 10005 ]

Ready for Pull Request [ 10304 ]

Nowlan Freese made changes - 25/Oct/18 4:36 PM

Assignee

Pranav Sanjay Tambvekar [ ptambvek ]

Pranav Sanjay Tambvekar (Inactive) made changes - 25/Oct/18 4:45 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Nowlan Freese made changes - 25/Oct/18 6:31 PM

Status

Pull Request Submitted [ 10101 ]

Reviewing [ 10301 ]

Nowlan Freese made changes - 29/Oct/18 1:22 PM

Attachment		example.bed [ 14182 ]
Attachment		soft-match-deletion-match-insertion-match-soft.sam [ 14183 ]

Nowlan Freese made changes - 30/Oct/18 10:45 AM

Attachment

VCF_HomoSapien_EDITED.vcf [ 14184 ]

Pranav Sanjay Tambvekar (Inactive) made changes - 30/Oct/18 4:43 PM

Status

Reviewing [ 10301 ]

Needs 1st Level Review [ 10005 ]

Pranav Sanjay Tambvekar (Inactive) made changes - 30/Oct/18 4:44 PM

Assignee

Pranav Sanjay Tambvekar [ ptambvek ]

Nowlan Freese made changes - 30/Oct/18 4:55 PM

Status

Needs 1st Level Review [ 10005 ]

Reviewing [ 10301 ]

Nowlan Freese made changes - 30/Oct/18 4:55 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 30/Oct/18 5:27 PM

Status

Reviewing [ 10301 ]

Ready for Pull Request [ 10304 ]

Nowlan Freese made changes - 30/Oct/18 5:27 PM

Assignee

Nowlan Freese [ nfreese ]

Pranav Sanjay Tambvekar [ ptambvek ]

Pranav Sanjay Tambvekar (Inactive) made changes - 30/Oct/18 6:31 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Nowlan Freese made changes - 31/Oct/18 12:15 PM

Status

Pull Request Submitted [ 10101 ]

Reviewing [ 10301 ]

Nowlan Freese made changes - 31/Oct/18 12:16 PM

Attachment

GFF3_example_1_EDITED.gff3 [ 14185 ]

Nowlan Freese made changes - 31/Oct/18 12:21 PM

Attachment

GFF3_example_1_EDITED_negative.gff3 [ 14186 ]

Ann Loraine made changes - 12/Nov/18 3:17 PM

Rank

Ranked higher

Ann Loraine made changes - 12/Nov/18 3:20 PM

Sprint

Fall 2018 Sprint 4 [ 54 ]

Fall 2018 Sprint 4, Fall 2018 Sprint 5 [ 54, 55 ]

Ann Loraine made changes - 12/Nov/18 3:20 PM

Rank

Ranked higher

Ann Loraine made changes - 16/Nov/18 4:08 PM

Fix Version/s

9.1.0 Major Release [ 10601 ]

Ann Loraine made changes - 29/Nov/18 8:05 AM

Rank

Ranked higher

Ann Loraine made changes - 29/Nov/18 8:10 AM

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 - 29/Nov/18 8:10 AM

Rank

Ranked higher

Ann Loraine made changes - 11/Dec/18 4:49 PM

Status

Reviewing [ 10301 ]

Needs Testing [ 10002 ]

Ann Loraine made changes - 13/Dec/18 3:02 PM

Rank

Ranked higher

Ann Loraine made changes - 13/Dec/18 3:03 PM

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 - 13/Dec/18 3:27 PM

Assignee

Pranav Sanjay Tambvekar [ ptambvek ]

Srishtee Marotkar [ srishtee ]

Srishtee Marotkar (Inactive) made changes - 14/Dec/18 9:50 AM

Status

Needs Testing [ 10002 ]

Testing In Progress [ 10003 ]

Srishtee Marotkar (Inactive) made changes - 18/Dec/18 5:55 PM

Attachment

IGBF1441_Testing.docx [ 14202 ]

Srishtee Marotkar (Inactive) made changes - 18/Dec/18 5:57 PM

Comment

[ Details for Failed Test Cases ]

Srishtee Marotkar (Inactive) made changes - 18/Dec/18 6:12 PM

Status

Testing In Progress [ 10003 ]

Open [ 1 ]

Srishtee Marotkar (Inactive) made changes - 18/Dec/18 6:12 PM

Assignee

Srishtee Marotkar [ srishtee ]

Ann Loraine made changes - 21/Dec/18 1:29 PM

Rank

Ranked higher

Ann Loraine made changes - 21/Dec/18 1:30 PM

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 - 09/Jan/19 1:02 PM

Status

Open [ 1 ]

In Progress [ 3 ]

Nowlan Freese made changes - 09/Jan/19 1:03 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 09/Jan/19 2:38 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 09/Jan/19 2:38 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 09/Jan/19 2:39 PM

Assignee

Srishtee Marotkar [ srishteem ]

Srishtee Marotkar (Inactive) made changes - 10/Jan/19 2:00 PM

Attachment

IGBF1441_Review_Screenshot.PNG [ 14204 ]

Srishtee Marotkar (Inactive) made changes - 10/Jan/19 2:00 PM

Status

Needs 1st Level Review [ 10005 ]

Ready for Pull Request [ 10304 ]

Srishtee Marotkar (Inactive) made changes - 10/Jan/19 2:00 PM

Assignee

Srishtee Marotkar [ srishteem ]

Nowlan Freese [ nfreese ]

Ann Loraine made changes - 30/Jan/19 12:00 PM

Rank

Ranked higher

Ann Loraine made changes - 30/Jan/19 12:02 PM

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 - 30/Jan/19 12:02 PM

Rank

Ranked higher

Nowlan Freese made changes - 31/Jan/19 4:22 PM

Assignee

Nowlan Freese [ nfreese ]

Kiran Korey [ kkorey ]

Nowlan Freese made changes - 31/Jan/19 4:22 PM

Assignee

Kiran Korey [ kkorey ]

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 05/Feb/19 4:53 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Nowlan Freese made changes - 05/Feb/19 4:56 PM

Attachment

softClip-DepthGraphStart-CORRECT.png [ 14241 ]

Ann Loraine made changes - 05/Feb/19 5:28 PM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 05/Feb/19 5:28 PM

Assignee

Nowlan Freese [ nfreese ]

Ann Loraine [ aloraine ]

Ann Loraine made changes - 05/Feb/19 5:29 PM

Status

Reviewing Pull Request [ 10303 ]

Needs Testing [ 10002 ]

Ann Loraine made changes - 05/Feb/19 5:29 PM

Assignee

Ann Loraine [ aloraine ]

Sai Charan Reddy Vallapureddy (Inactive) made changes - 15/Feb/19 10:46 AM

Resolution		Done [ 10000 ]
Status	Needs Testing [ 10002 ]	Closed [ 6 ]

Nowlan Freese made changes - 15/Feb/19 11:39 AM

Assignee

Pranav Sanjay Tambvekar [ ptambvek ]

Sai Charan Reddy Vallapureddy (Inactive) made changes - 15/Feb/19 11:39 AM

Assignee

Pranav Sanjay Tambvekar [ ptambvek ]

Srishtee Marotkar [ srishteem ]

Ann Loraine made changes - 27/Aug/19 4:59 PM

Workflow

Loraine Lab Workflow [ 18147 ]

Fall 2019 Workflow Update [ 19967 ]

Ann Loraine made changes - 16/Oct/19 5:49 PM

Workflow

Fall 2019 Workflow Update [ 19967 ]

Revised Fall 2019 Workflow Update [ 22088 ]

Nowlan Freese made changes - 13/Nov/19 3:01 PM

Assignee

Srishtee Marotkar [ srishteem ]

Nowlan Freese [ nfreese ]

People

Assignee:

Nowlan Freese

Reporter:

Nowlan Freese

Votes:

0 Vote for this issue

Watchers:

5 Start watching this issue

Dates

Created:

24/Oct/18 10:11 AM

Updated:

13/Nov/19 3:01 PM

Resolved:

15/Feb/19 10:46 AM