[IGBF-4219] Fix loading remote VCF files - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
4
Epic Link:
Improve VCF in IGB
Sprint:
Fall 1, Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6, Fall 2

Description

Situation: Current implementation is failing when trying to load VCF from Quickload

Issue eloboration:
New implementation is using VCFFileReader not lineReader, which can process only local files not any kind of URL (http)

UPDATE: The issue was with loading VCF file via URL. I do not think the issue was due to the file being part of a Quickload.

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Screenshot 2025-06-26 at 1.50.51 PM.png
389 kB
26/Jun/25 1:51 PM
vcf_fileerror_popup.png
77 kB
01/Jul/25 3:31 PM

Issue Links

relates to

IGBF-4106 Integrate htsjdk library for parsing VCF in IGB

Closed

IGBF-4166 Collect VCF files and test new vcf parsing

Closed

IGBF-4316 Use index files of VCF for faster loading time

Closed

Activity

Ascending order - Click to sort in descending order

saideepthi jagarapu (Inactive) created issue - 22/May/25 10:09 AM

saideepthi jagarapu (Inactive) made changes - 22/May/25 10:09 AM

Field	Original Value	New Value
Epic Link		IGBF-3836 [ 23135 ]

saideepthi jagarapu (Inactive) made changes - 22/May/25 10:09 AM

Link

This issue clones ~~IGBF-4166~~ [ ~~IGBF-4166~~ ]

saideepthi jagarapu (Inactive) made changes - 22/May/25 10:09 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

saideepthi jagarapu (Inactive) made changes - 22/May/25 10:10 AM

Description

Situation: Collect vcf files for testing changes

Task: Gather and test vcf files

saideepthi jagarapu (Inactive) made changes - 22/May/25 10:11 AM

Link

This issue relates to ~~IGBF-4166~~ [ ~~IGBF-4166~~ ]

saideepthi jagarapu (Inactive) made changes - 22/May/25 10:11 AM

Link

This issue clones ~~IGBF-4166~~ [ ~~IGBF-4166~~ ]

Ann Loraine made changes - 26/May/25 9:47 AM

Sprint

Spring 3, Spring 5, Spring 6, Spring 8 [ 212, 214, 215, 217 ]

Spring 3, Spring 5, Spring 6, Spring 8, Summer 1 [ 212, 214, 215, 217, 218 ]

Ann Loraine made changes - 26/May/25 9:47 AM

Rank

Ranked higher

Nowlan Freese made changes - 28/May/25 10:34 AM

Summary

VCF Quickload Issue

Fix VCF Quickload Issue

Nowlan Freese made changes - 30/May/25 10:34 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Nowlan Freese made changes - 05/Jun/25 10:32 AM

Sprint

Spring 3, Spring 5, Spring 6, Spring 8, Summer 1 [ 212, 214, 215, 217, 218 ]

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2 [ 212, 214, 215, 217, 219 ]

Ann Loraine made changes - 09/Jun/25 10:15 AM

Sprint

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2 [ 212, 214, 215, 217, 219 ]

Spring 3, Spring 5, Spring 6, Spring 8, Summer 3 [ 212, 214, 215, 217, 220 ]

Ann Loraine made changes - 09/Jun/25 10:15 AM

Rank

Ranked lower

saideepthi jagarapu (Inactive) made changes - 11/Jun/25 10:15 AM

Sprint

Spring 3, Spring 5, Spring 6, Spring 8, Summer 3 [ 212, 214, 215, 217, 220 ]

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2 [ 212, 214, 215, 217, 219 ]

saideepthi jagarapu (Inactive) made changes - 11/Jun/25 10:15 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 23/Jun/25 12:26 PM

Sprint

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2 [ 212, 214, 215, 217, 219 ]

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3 [ 212, 214, 215, 217, 219, 220 ]

Ann Loraine made changes - 23/Jun/25 12:26 PM

Rank

Ranked higher

saideepthi jagarapu (Inactive) made changes - 26/Jun/25 1:33 PM

Link

This issue relates to ~~IGBF-4106~~ [ ~~IGBF-4106~~ ]

saideepthi jagarapu (Inactive) made changes - 26/Jun/25 1:51 PM

Attachment

Screenshot 2025-06-26 at 1.50.51 PM.png [ 18734 ]

saideepthi jagarapu (Inactive) made changes - 01/Jul/25 3:31 PM

Attachment

vcf_fileerror_popup.png [ 18735 ]

saideepthi jagarapu (Inactive) made changes - 01/Jul/25 5:00 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

saideepthi jagarapu (Inactive) made changes - 02/Jul/25 9:55 AM

Assignee

saideepthi jagarapu [ sjagarap ]

Ann Loraine made changes - 05/Jul/25 11:34 AM

Sprint

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3 [ 212, 214, 215, 217, 219, 220 ]

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4 [ 212, 214, 215, 217, 219, 220, 221 ]

Ann Loraine made changes - 05/Jul/25 11:34 AM

Rank

Ranked higher

Paige Kulzer (Inactive) made changes - 11/Jul/25 9:54 AM

Assignee

Paige Kulzer [ pkulzer ]

Paige Kulzer (Inactive) made changes - 15/Jul/25 9:44 AM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 15/Jul/25 10:19 AM

Summary

Fix VCF Quickload Issue

Fix loading remote VCF files

Nowlan Freese made changes - 15/Jul/25 10:20 AM

Description

Situation: Current implementation is failing when trying to load VCF from Quickload

Issue eloboration:
New implementation is using VCFFileReader not lineReader, which can process only local files not any kind of URL (http)

UPDATE: The issue was with loading VCF file via URL. I do not think the issue was due to the file being part of a Quickload.

Paige Kulzer (Inactive) made changes - 16/Jul/25 10:12 AM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Paige Kulzer (Inactive) made changes - 16/Jul/25 10:12 AM

Assignee

Paige Kulzer [ pkulzer ]

saideepthi jagarapu [ sjagarap ]

Ann Loraine made changes - 21/Jul/25 10:04 AM

Sprint

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4 [ 212, 214, 215, 217, 219, 220, 221 ]

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 5 [ 212, 214, 215, 217, 219, 220, 221, 222 ]

Ann Loraine made changes - 21/Jul/25 10:04 AM

Rank

Ranked higher

Nowlan Freese made changes - 24/Jul/25 10:26 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 29/Jul/25 10:10 AM

Sprint

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 5 [ 212, 214, 215, 217, 219, 220, 221, 222 ]

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6 [ 212, 214, 215, 217, 219, 220, 221, 223 ]

Ann Loraine made changes - 06/Aug/25 9:42 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 18/Aug/25 10:33 AM

Sprint

Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6 [ 212, 214, 215, 217, 219, 220, 221, 223 ]

Testing 3 : 19 Nov - 29 Nov 2, Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6 [ 83, 212, 214, 215, 217, 219, 220, 221, 223 ]

Ann Loraine made changes - 18/Aug/25 10:33 AM

Rank

Ranked higher

saideepthi jagarapu (Inactive) made changes - 22/Aug/25 10:02 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 02/Sep/25 7:52 AM

Sprint

Fall 1, Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6 [ 83, 212, 214, 215, 217, 219, 220, 221, 223 ]

Fall 1, Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6, Fall 2 [ 83, 212, 214, 215, 217, 219, 220, 221, 223, 225 ]

Ann Loraine made changes - 02/Sep/25 7:52 AM

Rank

Ranked higher

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:25 PM

Link

This issue is cloned by ~~IGBF-4316~~ [ ~~IGBF-4316~~ ]

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:29 PM

Link

This issue relates to ~~IGBF-4316~~ [ ~~IGBF-4316~~ ]

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:29 PM

Link

This issue is cloned by ~~IGBF-4316~~ [ ~~IGBF-4316~~ ]

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:30 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:30 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:30 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:30 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:30 PM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:30 PM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:30 PM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

saideepthi jagarapu (Inactive) made changes - 09/Sep/25 1:30 PM

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

People

Assignee:

saideepthi jagarapu (Inactive)

Reporter:

saideepthi jagarapu (Inactive)

Votes:

0 Vote for this issue

Watchers:

3 Start watching this issue

Dates

Created:

22/May/25 10:09 AM

Updated:

09/Sep/25 1:30 PM

Resolved:

09/Sep/25 1:30 PM