rubam 0.3.12__tar.gz

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Files changed (134) hide show
  1. rubam-0.3.12/.gitattributes +16 -0
  2. rubam-0.3.12/.gitignore +93 -0
  3. rubam-0.3.12/CHANGELOG.md +783 -0
  4. rubam-0.3.12/CITATION.cff +26 -0
  5. rubam-0.3.12/CONTRIBUTING.md +133 -0
  6. rubam-0.3.12/Cargo.lock +1306 -0
  7. rubam-0.3.12/Cargo.toml +91 -0
  8. rubam-0.3.12/LICENSE +22 -0
  9. rubam-0.3.12/PKG-INFO +292 -0
  10. rubam-0.3.12/README.md +263 -0
  11. rubam-0.3.12/SECURITY.md +93 -0
  12. rubam-0.3.12/deny.toml +74 -0
  13. rubam-0.3.12/docs/bcftools_compatibility.md +78 -0
  14. rubam-0.3.12/docs/pysam_compatibility_matrix.md +199 -0
  15. rubam-0.3.12/docs/samtools_compatibility.md +90 -0
  16. rubam-0.3.12/docs/vcf_conformance_matrix.md +70 -0
  17. rubam-0.3.12/docs/wheel_smoke_test.md +156 -0
  18. rubam-0.3.12/docs/windows_native_stress.md +64 -0
  19. rubam-0.3.12/pyproject.toml +54 -0
  20. rubam-0.3.12/rubam/__init__.py +1029 -0
  21. rubam-0.3.12/rubam/_cli_shims.py +188 -0
  22. rubam-0.3.12/rubam/_tabix.py +157 -0
  23. rubam-0.3.12/rubam/cli.py +230 -0
  24. rubam-0.3.12/rubam/smoke_test.py +85 -0
  25. rubam-0.3.12/rubam/tools/__init__.py +77 -0
  26. rubam-0.3.12/rubam/tools/bcftools/__init__.py +110 -0
  27. rubam-0.3.12/src/alignment.rs +3460 -0
  28. rubam-0.3.12/src/api/aligned_segment.rs +196 -0
  29. rubam-0.3.12/src/api/alignment_file.rs +70 -0
  30. rubam-0.3.12/src/api/aux_data.rs +105 -0
  31. rubam-0.3.12/src/api/cigar.rs +90 -0
  32. rubam-0.3.12/src/api/error.rs +26 -0
  33. rubam-0.3.12/src/api/header.rs +50 -0
  34. rubam-0.3.12/src/api/mod.rs +17 -0
  35. rubam-0.3.12/src/bgzf_file.rs +207 -0
  36. rubam-0.3.12/src/bin/bcftools.rs +536 -0
  37. rubam-0.3.12/src/bin/depth.rs +114 -0
  38. rubam-0.3.12/src/bin/samtools.rs +337 -0
  39. rubam-0.3.12/src/bin/synth_bam.rs +302 -0
  40. rubam-0.3.12/src/common.rs +288 -0
  41. rubam-0.3.12/src/depth.rs +617 -0
  42. rubam-0.3.12/src/fasta_file.rs +214 -0
  43. rubam-0.3.12/src/fastx_file.rs +229 -0
  44. rubam-0.3.12/src/lib.rs +108 -0
  45. rubam-0.3.12/src/pileup.rs +271 -0
  46. rubam-0.3.12/src/pileup_iter.rs +46 -0
  47. rubam-0.3.12/src/stats.rs +210 -0
  48. rubam-0.3.12/src/tabix_file.rs +51 -0
  49. rubam-0.3.12/src/tools/bcftools/concat.rs +202 -0
  50. rubam-0.3.12/src/tools/bcftools/index.rs +173 -0
  51. rubam-0.3.12/src/tools/bcftools/mod.rs +14 -0
  52. rubam-0.3.12/src/tools/bcftools/norm.rs +627 -0
  53. rubam-0.3.12/src/tools/bcftools/query.rs +532 -0
  54. rubam-0.3.12/src/tools/bcftools/sort.rs +143 -0
  55. rubam-0.3.12/src/tools/bcftools/stats.rs +300 -0
  56. rubam-0.3.12/src/tools/bcftools/view.rs +330 -0
  57. rubam-0.3.12/src/tools/calmd.rs +70 -0
  58. rubam-0.3.12/src/tools/faidx.rs +64 -0
  59. rubam-0.3.12/src/tools/flagstat.rs +191 -0
  60. rubam-0.3.12/src/tools/idxstats.rs +60 -0
  61. rubam-0.3.12/src/tools/index.rs +31 -0
  62. rubam-0.3.12/src/tools/merge.rs +83 -0
  63. rubam-0.3.12/src/tools/mod.rs +16 -0
  64. rubam-0.3.12/src/tools/sort.rs +68 -0
  65. rubam-0.3.12/src/tools/view.rs +148 -0
  66. rubam-0.3.12/src/variant.rs +1864 -0
  67. rubam-0.3.12/tests/api_aligned_segment.rs +68 -0
  68. rubam-0.3.12/tests/api_alignment_file.rs +36 -0
  69. rubam-0.3.12/tests/api_aux.rs +35 -0
  70. rubam-0.3.12/tests/api_cigar.rs +69 -0
  71. rubam-0.3.12/tests/api_header.rs +43 -0
  72. rubam-0.3.12/tests/api_smoke.rs +16 -0
  73. rubam-0.3.12/tests/cargo_bcftools_cli.rs +183 -0
  74. rubam-0.3.12/tests/data/harmos_compat.bam +0 -0
  75. rubam-0.3.12/tests/data/harmos_compat.bam.bai +0 -0
  76. rubam-0.3.12/tests/data/harmos_compat.sam +13 -0
  77. rubam-0.3.12/tests/data/validation_3sample_100rec.vcf.gz +0 -0
  78. rubam-0.3.12/tests/data/validation_3sample_100rec.vcf.gz.tbi +0 -0
  79. rubam-0.3.12/tests/example.bam +0 -0
  80. rubam-0.3.12/tests/example.bam.bai +0 -0
  81. rubam-0.3.12/tests/fixtures/pysam_parity.bam +0 -0
  82. rubam-0.3.12/tests/fixtures/pysam_parity.bam.bai +0 -0
  83. rubam-0.3.12/tests/fixtures/smoke.bam +0 -0
  84. rubam-0.3.12/tests/fixtures/smoke.bam.bai +0 -0
  85. rubam-0.3.12/tests/harmos_compat.rs +139 -0
  86. rubam-0.3.12/tests/integration_test.rs +23 -0
  87. rubam-0.3.12/tests/proptest_cigar.rs +172 -0
  88. rubam-0.3.12/tests/proptest_depth.proptest-regressions +10 -0
  89. rubam-0.3.12/tests/proptest_depth.rs +411 -0
  90. rubam-0.3.12/tests/samtools_depth_options/expected.md +80 -0
  91. rubam-0.3.12/tests/samtools_depth_options/run_matrix.sh +300 -0
  92. rubam-0.3.12/tests/test_aligned_segment.py +125 -0
  93. rubam-0.3.12/tests/test_aligned_segment_setters.py +238 -0
  94. rubam-0.3.12/tests/test_alignment_file.py +208 -0
  95. rubam-0.3.12/tests/test_bam_write_builder.py +287 -0
  96. rubam-0.3.12/tests/test_bam_write_field_level.py +135 -0
  97. rubam-0.3.12/tests/test_bam_write_path.py +145 -0
  98. rubam-0.3.12/tests/test_bcftools_concat.py +98 -0
  99. rubam-0.3.12/tests/test_bcftools_index.py +109 -0
  100. rubam-0.3.12/tests/test_bcftools_norm.py +137 -0
  101. rubam-0.3.12/tests/test_bcftools_query.py +120 -0
  102. rubam-0.3.12/tests/test_bcftools_sort.py +98 -0
  103. rubam-0.3.12/tests/test_bcftools_stats.py +92 -0
  104. rubam-0.3.12/tests/test_bcftools_view.py +102 -0
  105. rubam-0.3.12/tests/test_cli_samtools.py +160 -0
  106. rubam-0.3.12/tests/test_core.py +69 -0
  107. rubam-0.3.12/tests/test_fasta_file.py +113 -0
  108. rubam-0.3.12/tests/test_features.py +112 -0
  109. rubam-0.3.12/tests/test_module_wrappers.py +132 -0
  110. rubam-0.3.12/tests/test_pileup_iter.py +19 -0
  111. rubam-0.3.12/tests/test_pysam_compat_v035_v038.py +573 -0
  112. rubam-0.3.12/tests/test_pysam_parity_findings.py +135 -0
  113. rubam-0.3.12/tests/test_tabix_file.py +97 -0
  114. rubam-0.3.12/tests/test_tools_calmd.py +51 -0
  115. rubam-0.3.12/tests/test_tools_faidx.py +34 -0
  116. rubam-0.3.12/tests/test_tools_idxstats.py +13 -0
  117. rubam-0.3.12/tests/test_tools_index.py +15 -0
  118. rubam-0.3.12/tests/test_tools_merge.py +27 -0
  119. rubam-0.3.12/tests/test_tools_smoke.py +16 -0
  120. rubam-0.3.12/tests/test_tools_sort.py +25 -0
  121. rubam-0.3.12/tests/test_tools_view.py +26 -0
  122. rubam-0.3.12/tests/test_validate_variants.py +45 -0
  123. rubam-0.3.12/tests/test_variant_file.py +572 -0
  124. rubam-0.3.12/tests/test_windows_native_stress.py +217 -0
  125. rubam-0.3.12/tests/vcf_conformance/__init__.py +0 -0
  126. rubam-0.3.12/tests/vcf_conformance/fixtures/format_complex.vcf +70 -0
  127. rubam-0.3.12/tests/vcf_conformance/fixtures/indels.vcf +226 -0
  128. rubam-0.3.12/tests/vcf_conformance/fixtures/missing_values.vcf +69 -0
  129. rubam-0.3.12/tests/vcf_conformance/fixtures/mnv.vcf +115 -0
  130. rubam-0.3.12/tests/vcf_conformance/fixtures/multi_allelic.vcf +68 -0
  131. rubam-0.3.12/tests/vcf_conformance/fixtures/multi_sample.vcf +68 -0
  132. rubam-0.3.12/tests/vcf_conformance/fixtures/phased_gt.vcf +66 -0
  133. rubam-0.3.12/tests/vcf_conformance/fixtures/snv_only.vcf +227 -0
  134. rubam-0.3.12/tests/vcf_conformance/test_conformance.py +294 -0
rubam-0.3.12/.gitattributes ADDED
@@ -0,0 +1,16 @@
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+ # Normalize line endings: text files are LF in the repo, checked out
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+ # natively. Keeps Windows checkouts from churning every source file.
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+ * text=auto eol=lf
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+
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+ # Binary fixtures and assets — never touch.
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+ *.bam binary
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+ *.bai binary
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+ *.cram binary
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+ *.crai binary
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+ *.pdf binary
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+ *.png binary
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+ *.pyd binary
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+ *.so binary
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+
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+ # Shell scripts must stay LF even on Windows checkouts.
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+ *.sh text eol=lf
rubam-0.3.12/.gitignore ADDED
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+ # Cargo build artifacts
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+ debug/
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+ target/
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+
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+ # Backup files generated by rustfmt
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+ **/*.rs.bk
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+
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+ # MSVC debugging info
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+ *.pdb
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+
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+ # IDE
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+ #.idea/
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+
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+ # Notebooks
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+ .ipynb
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+ .ipynb_*
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+ .ipynb_*/
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+ notebooks/
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+
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+ # Build helpers
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+ .develop.sh
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+
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+ # Python build outputs (the cdylib lives in rubam/_rubam.{pyd,so})
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+ *.so
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+ *.pyd
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+ __pycache__
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+ *.swp
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+
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+ # Python venvs
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+ .venv/
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+ venv/
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+
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+ # Datasets and bench outputs (huge — kept on D:\Victor\rubam\data and \results)
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+ data/
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+ results/
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+ *.bam
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+ *.bai
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+ *.cram
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+ *.crai
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+ *.fa
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+ *.fasta
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+ *.fa.fai
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+ *.fasta.fai
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+ *.fastq
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+ *.fastq.gz
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+ !tests/example.bam
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+ !tests/example.bam.bai
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+ !tests/data/
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+ !tests/data/harmos_compat.bam
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+ !tests/data/harmos_compat.bam.bai
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+ !tests/data/harmos_compat.sam
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+ !tests/fixtures/
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+ !tests/fixtures/*.bam
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+ !tests/fixtures/*.bai
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+
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+ # Local scratch / demo apps (not part of the published package)
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+ demo_app.py
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+ demanding_app.py
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+ scratch_demo.bam
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+
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+ # Author-local material kept out of the public software repo: research
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+ # paper, benchmark harness + outputs, dataset/setup scripts, container and
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+ # bench dependency manifests, and local agent/config files. These live on
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+ # the author's machine only and are not part of the rubam software.
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+ /CLAUDE.md
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+ /.claude/
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+ /bench/
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+ /paper/
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+ /scripts/
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+ /results/
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+ /requirements.txt
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+ /Dockerfile
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+ /.github/workflows/bench-cross-env.yml
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+
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+ # Pytest / coverage caches
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+ .pytest_cache/
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+ .coverage
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+ coverage.svg
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+
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+ # bioRxiv build outputs
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+ paper/*.aux
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+ paper/*.bbl
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+ paper/*.blg
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+ paper/*.log
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+ paper/*.out
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+ paper/*.toc
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+ paper/*.synctex.gz
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+ paper/_output/
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+ paper/_freeze/
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+ paper/.quarto/
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+ # LaTeX-generated figure PDFs are ignored, but matplotlib-generated
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+ # bench figures (committed alongside the paper text) are kept.
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+ # To regenerate: bench/plot_*.py against results/<run-id>/metrics.csv.