Coverage report: 97%

Files Functions Classes

coverage.py v7.7.1, created at 2025-03-25 21:02 +0000

File function statements missing excluded coverage
src/pangwas/__init__.py (no function) 3 0 0 100%
src/pangwas/pangwas.py get_options 242 0 0 100%
src/pangwas/pangwas.py check_output_dir 3 0 0 100%
src/pangwas/pangwas.py reverse_complement 7 0 0 100%
src/pangwas/pangwas.py extract_cli_param 11 0 0 100%
src/pangwas/pangwas.py run_cmd 18 0 0 100%
src/pangwas/pangwas.py annotate 26 26 0 0%
src/pangwas/pangwas.py extract 253 0 0 100%
src/pangwas/pangwas.py collect 65 0 0 100%
src/pangwas/pangwas.py cluster 47 1 0 98%
src/pangwas/pangwas.py defrag 101 0 0 100%
src/pangwas/pangwas.py summarize 457 18 0 96%
src/pangwas/pangwas.py run_mafft 2 2 0 0%
src/pangwas/pangwas.py align 209 3 0 99%
src/pangwas/pangwas.py get_ranges 3 0 0 100%
src/pangwas/pangwas.py collapse_ranges 15 0 0 100%
src/pangwas/pangwas.py structural 76 3 0 96%
src/pangwas/pangwas.py snps 210 0 0 100%
src/pangwas/pangwas.py presence_absence 33 0 0 100%
src/pangwas/pangwas.py combine 24 0 0 100%
src/pangwas/pangwas.py root_tree 57 3 0 95%
src/pangwas/pangwas.py root_tree_midpoint 26 4 0 85%
src/pangwas/pangwas.py read_tree 8 0 0 100%
src/pangwas/pangwas.py tree 77 0 0 100%
src/pangwas/pangwas.py get_delim 7 0 0 100%
src/pangwas/pangwas.py table_to_rtab 67 0 0 100%
src/pangwas/pangwas.py vcf_to_rtab 54 0 0 100%
src/pangwas/pangwas.py binarize 41 0 0 100%
src/pangwas/pangwas.py qq_plot 51 7 0 86%
src/pangwas/pangwas.py gwas 381 11 0 97%
src/pangwas/pangwas.py text_to_path 45 2 0 96%
src/pangwas/pangwas.py linear_scale 3 1 0 67%
src/pangwas/pangwas.py manhattan 417 3 0 99%
src/pangwas/pangwas.py heatmap 462 6 0 99%
src/pangwas/pangwas.py cli 32 7 0 78%
src/pangwas/pangwas.py (no function) 77 1 0 99%
Total   3610 98 0 97%

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