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Pull request overview
This PR adds multi-layer output generation in PretextMap, allowing separate layers to be produced based on MAPQ thresholds (optionally configured via --mapqLayers), and appending per-layer data to the output file with additional header metadata.
Changes:
- Introduces
mapq_layerstorage (per-threshold image sets + per-layer read counts) and routes read-pairs into all qualifying layers. - Adds
--mapqLayersCLI parsing (sorting + deduplication) and updates memory sizing to scale with the number of layers. - Extends the output header with optional layer metadata and updates texture writing/status output to be layer-aware.
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| global_variable | ||
| u32 | ||
| Min_Map_Quality = 10; | ||
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| #define Max_MapQ_Layers 16 | ||
| #define MapQ_Layer_Header_Extension_Size 18 | ||
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| struct | ||
| mapq_layer | ||
| { | ||
| u32 threshold; | ||
| volatile u64 totalGoodReads; | ||
| volatile u16 ***images; | ||
| }; | ||
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| global_variable | ||
| u32 | ||
| MapQ_Layer_Thresholds[Max_MapQ_Layers] = {10}; | ||
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| global_variable | ||
| u32 | ||
| Number_of_MapQ_Layers = 1; |
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c-zhou
approved these changes
Jul 2, 2026
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This PR adds support in PretextMap for generating separate layers based on mapping quality (MAPQ). By default, two layers are created: one for MAPQ ≥ 0 and one for MAPQ ≥ 10