Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:4
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Epic Link:
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Sprint:Fall 1, Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6, Fall 2, Fall 3, Fall 4, Fall 5
Description
Identified two related issues in IGB 10.2.0 involving the loading of VCF files, both of which are regressions from version 10.1.0. These issues negatively affect performance and functionality when working with large or indexed VCF datasets.
1. Performance and Memory Issue When Loading VCF Files
When loading larger VCF files (e.g., 1KG.chr22.anno.infocol.vcf.gz), IGB 10.2.0 exhibits significantly increased memory usage and may crash or freeze when navigating to a gene.
In IGB 10.1.0, loading this file and accessing gene-level data works as expected.
In IGB 10.2.0, it appears the entire file is being loaded into memory when "Load Data" is clicked, rather than just the in-frame genomic region (as was the behavior in 10.1.0).
This results in performance degradation and potential out-of-memory errors, especially with large datasets.
2.* Failure to Load Tabix-Indexed VCF Files*
When attempting to load a VCF file with an associated Tabix index (e.g., Genome in a Bottle VCF), IGB 10.2.0 throws the following error:
ClassCastException: VCFSymLoaderTabix cannot be cast to QuickLoadSymLoader
These same files load without issue in IGB 10.1.0.
This appears to be a class loading or module registration issue introduced in the newer version, likely related to recent changes in VCF parsing logic.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3836 [ 23135 ] |
| 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. |
identified two related issues in IGB 10.2.0 involving the loading of VCF files, both of which are regressions from version 10.1.0. These issues negatively affect performance and functionality when working with large or indexed VCF datasets.
1. Performance and Memory Issue When Loading VCF Files When loading larger VCF files (e.g., 1KG.chr22.anno.infocol.vcf.gz), IGB 10.2.0 exhibits significantly increased memory usage and may crash or freeze when navigating to a gene. In IGB 10.1.0, loading this file and accessing gene-level data works as expected. In IGB 10.2.0, it appears the entire file is being loaded into memory when "Load Data" is clicked, rather than just the in-frame genomic region (as was the behavior in 10.1.0). This results in performance degradation and potential out-of-memory errors, especially with large datasets. 2. Failure to Load Tabix-Indexed VCF Files When attempting to load a VCF file with an associated Tabix index (e.g., Genome in a Bottle VCF), IGB 10.2.0 throws the following error: ClassCastException: VCFSymLoaderTabix cannot be cast to QuickLoadSymLoader These same files load without issue in IGB 10.1.0. This appears to be a class loading or module registration issue introduced in the newer version, likely related to recent changes in VCF parsing logic. |
| Description |
identified two related issues in IGB 10.2.0 involving the loading of VCF files, both of which are regressions from version 10.1.0. These issues negatively affect performance and functionality when working with large or indexed VCF datasets.
1. Performance and Memory Issue When Loading VCF Files When loading larger VCF files (e.g., 1KG.chr22.anno.infocol.vcf.gz), IGB 10.2.0 exhibits significantly increased memory usage and may crash or freeze when navigating to a gene. In IGB 10.1.0, loading this file and accessing gene-level data works as expected. In IGB 10.2.0, it appears the entire file is being loaded into memory when "Load Data" is clicked, rather than just the in-frame genomic region (as was the behavior in 10.1.0). This results in performance degradation and potential out-of-memory errors, especially with large datasets. 2. Failure to Load Tabix-Indexed VCF Files When attempting to load a VCF file with an associated Tabix index (e.g., Genome in a Bottle VCF), IGB 10.2.0 throws the following error: ClassCastException: VCFSymLoaderTabix cannot be cast to QuickLoadSymLoader These same files load without issue in IGB 10.1.0. This appears to be a class loading or module registration issue introduced in the newer version, likely related to recent changes in VCF parsing logic. |
Identified two related issues in IGB 10.2.0 involving the loading of VCF files, both of which are regressions from version 10.1.0. These issues negatively affect performance and functionality when working with large or indexed VCF datasets.
1. *Performance and Memory Issue When Loading VCF Files* When loading larger VCF files (e.g., 1KG.chr22.anno.infocol.vcf.gz), IGB 10.2.0 exhibits significantly increased memory usage and may crash or freeze when navigating to a gene. In IGB 10.1.0, loading this file and accessing gene-level data works as expected. In IGB 10.2.0, it appears the entire file is being loaded into memory when "Load Data" is clicked, rather than just the in-frame genomic region (as was the behavior in 10.1.0). This results in performance degradation and potential out-of-memory errors, especially with large datasets. 2.* Failure to Load Tabix-Indexed VCF Files* When attempting to load a VCF file with an associated Tabix index (e.g., Genome in a Bottle VCF), IGB 10.2.0 throws the following error: ClassCastException: VCFSymLoaderTabix cannot be cast to QuickLoadSymLoader These same files load without issue in IGB 10.1.0. This appears to be a class loading or module registration issue introduced in the newer version, likely related to recent changes in VCF parsing logic. |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | 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 ] | Fall 1, Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6, Fall 2, Fall 3 [ 83, 212, 214, 215, 217, 219, 220, 221, 223, 225, 226 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Paige Kulzer [ pkulzer ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Paige Kulzer [ pkulzer ] | saideepthi jagarapu [ sjagarap ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] | Nowlan Freese [ nfreese ] |
| Sprint | Fall 1, Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6, Fall 2, Fall 3 [ 83, 212, 214, 215, 217, 219, 220, 221, 223, 225, 226 ] | Fall 1, Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6, Fall 2, Fall 3, Fall 4 [ 83, 212, 214, 215, 217, 219, 220, 221, 223, 225, 226, 227 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] | saideepthi jagarapu [ sjagarap ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] | Paige Kulzer [ pkulzer ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Paige Kulzer [ pkulzer ] | saideepthi jagarapu [ sjagarap ] |
| Sprint | Fall 1, Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6, Fall 2, Fall 3, Fall 4 [ 83, 212, 214, 215, 217, 219, 220, 221, 223, 225, 226, 227 ] | Fall 1, Spring 3, Spring 5, Spring 6, Spring 8, Summer 2, Summer 3, Summer 4, Summer 6, Fall 2, Fall 3, Fall 4, Fall 5 [ 83, 212, 214, 215, 217, 219, 220, 221, 223, 225, 226, 227, 228 ] |
| Rank | Ranked higher |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Paige Kulzer [ pkulzer ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Paige Kulzer [ pkulzer ] | saideepthi jagarapu [ sjagarap ] |