[IGBF-1443] Implement Depth Graph (Soft-clip) - JIRA UNCC

Details

Type: New Feature
Status: Closed (View Workflow)
Priority: Minor
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
- Intermediate

Story Points:
2.5
Epic Link:
Improve IGB for users
Sprint:
Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep

Description

The track operation Depth Graph (All) is used to summarize the depth of reads. It does not include soft-clipped parts of the read.

Add Depth Graph (Soft-clip) as a track operation for bam/sam. This would create a depth graph for just soft-clip parts of reads.

This should be possible to do by copying how Depth Graph (All) functions, but using only syms of instance BamSoftChildSingletonSeqSym.

Attachments

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Attachments

Leaf1.small.aligned.sorted.softClipped.bam
651 kB
31/Aug/20 11:06 AM
Leaf1.small.aligned.sorted.softClipped.bam.bai
33 kB
31/Aug/20 11:06 AM
softClip.bam
0.2 kB
31/Aug/20 11:06 AM
softClip.bam.bai
0.1 kB
31/Aug/20 11:06 AM
SoftClip.png
960 kB
09/Sep/20 6:27 PM

Issue Links

relates to

IGBF-2523 Investigate: Is it possible to implement IGBF-1443 as an App that can run in IGB 9.1.4

Closed

IGBF-2647 Soft Clip Depth Graph incorrect for PacBio files

To-Do

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 10:44 AM

Nowlan Freese made changes - 24/Oct/18 10:44 AM

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

Ann Loraine made changes - 27/Aug/19 4:58 PM

Workflow

Loraine Lab Workflow [ 18149 ]

Fall 2019 Workflow Update [ 18915 ]

Ann Loraine made changes - 16/Oct/19 5:48 PM

Workflow	Fall 2019 Workflow Update [ 18915 ]	Revised Fall 2019 Workflow Update [ 21042 ]
Status	Open [ 1 ]	To-Do [ 10305 ]

Ann Loraine made changes - 13/Jul/20 8:24 AM

Epic Link

IGBF-1765 [ 17855 ]

Ann Loraine made changes - 13/Jul/20 8:24 AM

Story Points	5	2.5
Sprint		Summer 4: 14 Jul - 28 Jul [ 99 ]
Labels		Intermediate

Ann Loraine made changes - 16/Jul/20 4:00 PM

Sprint

Summer 4: 14 Jul - 28 Jul [ 99 ]

Ann Loraine made changes - 16/Jul/20 4:00 PM

Rank

Ranked higher

Ann Loraine made changes - 27/Jul/20 8:10 AM

Sprint

Summer 5: 29 Jul - 12 Aug [ 100 ]

Ann Loraine made changes - 27/Jul/20 8:10 AM

Rank

Ranked higher

Ann Loraine made changes - 17/Aug/20 9:25 AM

Rank

Ranked higher

Ann Loraine made changes - 17/Aug/20 9:50 AM

Sprint

Summer 5: 3 Aug - 14 Aug [ 100 ]

Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug [ 100, 101 ]

Ann Loraine made changes - 17/Aug/20 9:50 AM

Rank

Ranked higher

Jay Chamma (Inactive) made changes - 17/Aug/20 2:50 PM

Assignee

Jay Chamma [ gchamma ]

Jay Chamma (Inactive) made changes - 18/Aug/20 10:02 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Jay Chamma (Inactive) made changes - 19/Aug/20 9:54 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Jay Chamma (Inactive) made changes - 19/Aug/20 9:55 AM

Assignee

Jay Chamma [ gchamma ]

Ann Loraine made changes - 19/Aug/20 10:10 AM

Rank

Ranked higher

Philip Badzuh (Inactive) made changes - 21/Aug/20 1:22 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Philip Badzuh (Inactive) made changes - 21/Aug/20 1:22 PM

Assignee

Philip Badzuh [ pbadzuh ]

Ann Loraine made changes - 30/Aug/20 12:30 PM

Sprint

Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug [ 100, 101 ]

Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep [ 100, 101, 102 ]

Ann Loraine made changes - 30/Aug/20 12:30 PM

Rank

Ranked higher

Philip Badzuh (Inactive) made changes - 31/Aug/20 11:06 AM

Attachment		Leaf1.small.aligned.sorted.softClipped.bam [ 14848 ]
Attachment		Leaf1.small.aligned.sorted.softClipped.bam.bai [ 14849 ]
Attachment		softClip.bam [ 14850 ]
Attachment		softClip.bam.bai [ 14851 ]

Philip Badzuh (Inactive) made changes - 31/Aug/20 11:07 AM

Assignee

Philip Badzuh [ pbadzuh ]

Sai Supreeth Segu [ ssegu ]

Philip Badzuh (Inactive) made changes - 31/Aug/20 11:07 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Sai Supreeth Segu (Inactive) made changes - 01/Sep/20 12:14 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Sai Supreeth Segu (Inactive) made changes - 09/Sep/20 6:27 PM

Attachment

SoftClip.png [ 14857 ]

Sai Supreeth Segu (Inactive) made changes - 09/Sep/20 6:30 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Sai Supreeth Segu (Inactive) made changes - 09/Sep/20 6:30 PM

Assignee

Sai Supreeth Segu [ ssegu ]

Ann Loraine made changes - 10/Sep/20 12:42 AM

Link

This issue relates to ~~IGBF-2523~~ [ ~~IGBF-2523~~ ]

Nowlan Freese made changes - 11/Sep/20 9:14 AM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 11/Sep/20 9:14 AM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 11/Sep/20 11:09 AM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

Nowlan Freese made changes - 11/Sep/20 11:09 AM

Assignee

Nowlan Freese [ nfreese ]

Sai Supreeth Segu [ ssegu ]

Sai Supreeth Segu (Inactive) made changes - 11/Sep/20 11:18 AM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Sai Supreeth Segu (Inactive) made changes - 11/Sep/20 11:18 AM

Assignee

Sai Supreeth Segu [ ssegu ]

Ann Loraine made changes - 15/Sep/20 7:54 AM

Sprint

Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep [ 100, 101, 102 ]

Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep [ 100, 101, 102, 103 ]

Ann Loraine made changes - 15/Sep/20 7:54 AM

Rank

Ranked higher

Ann Loraine made changes - 15/Sep/20 12:37 PM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 15/Sep/20 12:37 PM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

Nowlan Freese made changes - 17/Sep/20 9:34 AM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Nowlan Freese made changes - 17/Sep/20 9:34 AM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 17/Sep/20 12:00 PM

Assignee

Nowlan Freese [ nfreese ]

Sai Supreeth Segu [ ssegu ]

Nowlan Freese made changes - 17/Sep/20 12:00 PM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

Nowlan Freese made changes - 17/Nov/20 10:31 AM

Fix Version/s

9.1.6 Major Release [ 10604 ]

Nowlan Freese made changes - 19/Nov/20 10:00 AM

Link

This issue relates to IGBF-2647 [ IGBF-2647 ]

Ann Loraine made changes - 30/Nov/20 12:06 PM

Fix Version/s

9.1.6 Major Release [ 10604 ]

People

Assignee:

Sai Supreeth Segu (Inactive)

Reporter:

Nowlan Freese

Votes:

0 Vote for this issue

Watchers:

4 Start watching this issue

Dates

Created:

24/Oct/18 10:44 AM

Updated:

30/Nov/20 12:06 PM

Resolved:

17/Sep/20 12:00 PM