[IGBF-1291] Show soft-clipped bases in BAM files - JIRA UNCC

Details

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

Story Points:
10
Sprint:
B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3, Fall 2018 Sprint 4

Description

IGB should show soft-clipped bases in BAM files.

Attachments

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Attachments

Leaf1.small.aligned.sorted.softClipped.bam
651 kB
28/Sep/18 4:02 PM
Leaf1.small.aligned.sorted.softClipped.bam.bai
33 kB
28/Sep/18 4:02 PM
softclip_igv.png
44 kB
28/Jun/18 1:41 PM
softClipExample.png
106 kB
28/Sep/18 3:59 PM
SoftClipped.png
435 kB
05/Jul/18 1:52 AM

Issue Links

relates to

IGBF-1440 Fix soft-clipping glyph render

Closed

IGBF-1441 Fix Depth Graph (Start) Soft-clip coordinates

Closed

IGBF-1443 Implement Depth Graph (Soft-clip)

Closed

IGBF-1422 Find example data sets where soft clipping reveals polymorphisms

Closed

IGBF-1442 Preserve soft-clip settings between sessions

Closed

IGBF-1447 Implement selectable deletion glyph

To-Do

IGBF-1222 Check if IGB shows soft-clipped bases from read alignments correctly

Closed

Show 2 more links (2 relates to)

Activity

Ascending order - Click to sort in descending order

Ann Loraine created issue - 14/Jun/18 3:06 PM

Ann Loraine made changes - 14/Jun/18 3:06 PM

Field	Original Value	New Value
Link		This issue relates to ~~IGBF-1222~~ [ ~~IGBF-1222~~ ]

Kiran Korey (Inactive) made changes - 28/Jun/18 1:41 PM

Attachment

soft.png [ 14102 ]

Kiran Korey (Inactive) made changes - 28/Jun/18 1:41 PM

Attachment

soft.png [ 14102 ]

Kiran Korey (Inactive) made changes - 28/Jun/18 1:41 PM

Attachment

softclip_igv.png [ 14103 ]

Ann Loraine made changes - 29/Jun/18 10:45 AM

Status

Open [ 1 ]

In Progress [ 3 ]

Ann Loraine made changes - 05/Jul/18 1:32 AM

Rank

Ranked higher

Ann Loraine made changes - 05/Jul/18 1:34 AM

Sprint

B - Summer 2018 [ 48 ]

B - Summer 2018, Summer 2018 Part 2 [ 48, 49 ]

Ann Loraine made changes - 05/Jul/18 1:34 AM

Rank

Ranked higher

Ann Loraine made changes - 05/Jul/18 1:52 AM

Attachment

SoftClipped.png [ 14116 ]

Ann Loraine made changes - 05/Jul/18 2:14 AM

Labels

Advanced

Ann Loraine made changes - 05/Jul/18 2:35 PM

Summary

Correct how IGB shows soft-clipped bases in BAM files

Allow showing soft-clipped bases in BAM files

Ann Loraine made changes - 05/Jul/18 2:35 PM

Summary

Allow showing soft-clipped bases in BAM files

Show soft-clipped bases in BAM files

Kiran Korey (Inactive) made changes - 17/Jul/18 9:57 AM

Status

In Progress [ 3 ]

Open [ 1 ]

Kiran Korey (Inactive) made changes - 24/Jul/18 9:21 AM

Status

Open [ 1 ]

In Progress [ 3 ]

Kiran Korey (Inactive) made changes - 27/Jul/18 1:32 PM

Status

In Progress [ 3 ]

Open [ 1 ]

Ann Loraine made changes - 31/Jul/18 9:55 AM

Rank

Ranked higher

Ann Loraine made changes - 31/Jul/18 9:57 AM

Sprint

B - Summer 2018, Summer 2018 Part 2 [ 48, 49 ]

B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3 [ 48, 49, 50 ]

Ann Loraine made changes - 31/Jul/18 9:57 AM

Rank

Ranked higher

Ann Loraine made changes - 31/Jul/18 10:06 AM

Story Points

Ann Loraine made changes - 07/Aug/18 9:37 AM

Status

Open [ 1 ]

In Progress [ 3 ]

Ann Loraine made changes - 07/Aug/18 9:37 AM

Assignee

Kiran Korey [ kkorey ]

Ann Loraine [ aloraine ]

Ann Loraine made changes - 14/Aug/18 11:57 AM

Assignee

Ann Loraine [ aloraine ]

Anh Moss [ aduong ]

Ann Loraine made changes - 14/Aug/18 4:48 PM

Rank

Ranked higher

Ann Loraine made changes - 14/Aug/18 4:49 PM

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 ]

Ann Loraine made changes - 30/Aug/18 1:17 PM

Rank

Ranked higher

Ann Loraine made changes - 30/Aug/18 1:20 PM

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 ]

Ann Loraine made changes - 30/Aug/18 1:20 PM

Rank

Ranked higher

Ann Loraine made changes - 20/Sep/18 4:13 AM

Rank

Ranked higher

Ann Loraine made changes - 20/Sep/18 4:14 AM

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 ]

Ann Loraine made changes - 20/Sep/18 3:21 PM

Assignee

Anh Moss [ aduong ]

Ann Loraine [ aloraine ]

Ann Loraine made changes - 20/Sep/18 3:21 PM

Assignee

Ann Loraine [ aloraine ]

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 28/Sep/18 2:12 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 28/Sep/18 2:13 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 28/Sep/18 2:14 PM

Status

Needs 1st Level Review [ 10005 ]

Pull Request Submitted [ 10101 ]

Nowlan Freese made changes - 28/Sep/18 3:40 PM

Status

Pull Request Submitted [ 10101 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 28/Sep/18 3:59 PM

Attachment

softClipExample.png [ 14156 ]

Nowlan Freese made changes - 28/Sep/18 4:02 PM

Attachment		Leaf1.small.aligned.sorted.softClipped.bam [ 14157 ]
Attachment		Leaf1.small.aligned.sorted.softClipped.bam.bai [ 14158 ]

Anh Moss (Inactive) made changes - 03/Oct/18 9:32 AM

Link

This issue relates to ~~IGBF-1422~~ [ ~~IGBF-1422~~ ]

Nowlan Freese made changes - 04/Oct/18 8:37 AM

Status

Needs 1st Level Review [ 10005 ]

In Progress [ 3 ]

Nowlan Freese made changes - 04/Oct/18 8:37 AM

Assignee

Nowlan Freese [ nfreese ]

Ann Loraine made changes - 22/Oct/18 10:08 AM

Rank

Ranked higher

Ann Loraine made changes - 22/Oct/18 10:09 AM

Sprint

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 ]

B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3, Fall 2018 Sprint 4 [ 48, 49, 50, 51, 52, 53, 54 ]

Ann Loraine made changes - 22/Oct/18 10:09 AM

Rank

Ranked higher

Ann Loraine made changes - 23/Oct/18 9:24 AM

Status

In Progress [ 3 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 23/Oct/18 9:24 AM

Status

Reviewing Pull Request [ 10303 ]

Needs Testing [ 10002 ]

Ann Loraine made changes - 23/Oct/18 9:24 AM

Rank

Ranked higher

Ann Loraine made changes - 23/Oct/18 9:25 AM

Assignee

Nowlan Freese [ nfreese ]

Srishti Tiwari (Inactive) made changes - 23/Oct/18 12:54 PM

Assignee

Srishti Tiwari [ stiwari8 ]

Nowlan Freese made changes - 24/Oct/18 9:03 AM

Link

This issue is blocked by ~~IGBF-1440~~ [ ~~IGBF-1440~~ ]

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

Link

This issue is blocked by ~~IGBF-1441~~ [ ~~IGBF-1441~~ ]

Nowlan Freese made changes - 24/Oct/18 10:31 AM

Link

This issue relates to IGBF-1442 [ IGBF-1442 ]

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

Link

This issue relates to ~~IGBF-1441~~ [ ~~IGBF-1441~~ ]

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

Link

This issue relates to ~~IGBF-1440~~ [ ~~IGBF-1440~~ ]

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

Link

This issue is blocked by ~~IGBF-1441~~ [ ~~IGBF-1441~~ ]

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

Link

This issue is blocked by ~~IGBF-1440~~ [ ~~IGBF-1440~~ ]

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

Link

This issue relates to ~~IGBF-1443~~ [ ~~IGBF-1443~~ ]

Srishti Tiwari (Inactive) made changes - 25/Oct/18 12:52 PM

Status

Needs Testing [ 10002 ]

Testing In Progress [ 10003 ]

Srishti Tiwari (Inactive) made changes - 25/Oct/18 4:51 PM

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

Nowlan Freese made changes - 29/Oct/18 12:27 PM

Link

This issue relates to IGBF-1447 [ IGBF-1447 ]

Ann Loraine made changes - 07/Nov/18 2:14 PM

Fix Version/s

9.0.2 Minor Release [ 10600 ]

Ann Loraine made changes - 16/Nov/18 4:06 PM

Fix Version/s

9.1.0 Major Release [ 10601 ]

Nowlan Freese made changes - 14/Jan/19 9:23 AM

Link

This issue relates to IGBF-9 [ IGBF-9 ]

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

Workflow

Loraine Lab Workflow [ 17982 ]

Fall 2019 Workflow Update [ 19881 ]

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

Workflow

Fall 2019 Workflow Update [ 19881 ]

Revised Fall 2019 Workflow Update [ 22000 ]

Nowlan Freese made changes - 13/Nov/19 3:03 PM

Assignee

Srishti Tiwari [ stiwari8 ]

Nowlan Freese [ nfreese ]

People

Assignee:

Nowlan Freese

Reporter:

Ann Loraine

Votes:

0 Vote for this issue

Watchers:

4 Start watching this issue

Dates

Created:

14/Jun/18 3:06 PM

Updated:

13/Nov/19 3:03 PM

Resolved:

25/Oct/18 4:51 PM