fix: dedupe error 13 #1447
fix: dedupe error 13 #1447
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… enhancing error handling
… enhancing error handling
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Pull Request Overview
This PR refactors the ATAC-seq fragment processing functions to improve code organization, error handling, and maintainability. The changes consolidate duplicate pipeline logic and provide more robust subprocess management.
- Refactored
prepare_fragment()anddeduplicate_fragment_rows()functions to use a shared pipeline infrastructure - Introduced helper functions for command building, tool validation, and subprocess execution
- Improved error handling and resource cleanup for subprocess pipelines
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #1447 +/- ##
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+ Coverage 88.50% 89.01% +0.50%
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Files 23 23
Lines 2662 2703 +41
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+ Hits 2356 2406 +50
+ Misses 306 297 -9
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Pull Request Overview
Copilot reviewed 1 out of 1 changed files in this pull request and generated 5 comments.
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| :return: Percentage of memory to allocate per sort thread. | ||
| """ | ||
| return max(sort_memory_percent // num_cores, 1) # ensure at least 1% memory per core | ||
| effective_memory_pct = min(sort_memory_percent, 50) if num_cores > 1 else sort_memory_percent |
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The hardcoded 50% memory cap lacks explanation. This magic number should be documented or made configurable, as different environments may benefit from different memory limits.
…U detection and memory calculation
This Pr fixes an issue where sorting the fragment was crashing when calling
pigzfor compression. This was only observed when sorting fragments larger than can fit into memory.This PR refactors the ATAC-seq fragment processing functions to improve code organization, error handling, and maintainability. The changes consolidate duplicate pipeline logic and provide more robust subprocess management.
Refactored prepare_fragment() and deduplicate_fragment_rows() functions to use a shared pipeline infrastructure
Introduced helper functions for command building, tool validation, and subprocess execution
Improved error handling and resource cleanup for subprocess pipelines
This will require a 6.x release