countmut 0.2.3__tar.gz → 0.2.4__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (49) hide show
  1. {countmut-0.2.3/countmut.egg-info → countmut-0.2.4}/PKG-INFO +1 -1
  2. {countmut-0.2.3 → countmut-0.2.4}/backend/countmut_core_main.c +1 -0
  3. {countmut-0.2.3 → countmut-0.2.4}/countmut/_core/countmut_core +0 -0
  4. {countmut-0.2.3 → countmut-0.2.4/countmut.egg-info}/PKG-INFO +1 -1
  5. {countmut-0.2.3 → countmut-0.2.4}/pyproject.toml +1 -1
  6. {countmut-0.2.3 → countmut-0.2.4}/LICENSE +0 -0
  7. {countmut-0.2.3 → countmut-0.2.4}/MANIFEST.in +0 -0
  8. {countmut-0.2.3 → countmut-0.2.4}/README.md +0 -0
  9. {countmut-0.2.3 → countmut-0.2.4}/backend/Makefile +0 -0
  10. {countmut-0.2.3 → countmut-0.2.4}/backend/bedidx.c +0 -0
  11. {countmut-0.2.3 → countmut-0.2.4}/backend/bgzf.c +0 -0
  12. {countmut-0.2.3 → countmut-0.2.4}/backend/bgzf.h +0 -0
  13. {countmut-0.2.3 → countmut-0.2.4}/backend/countmut_core.c +0 -0
  14. {countmut-0.2.3 → countmut-0.2.4}/backend/countmut_core.h +0 -0
  15. {countmut-0.2.3 → countmut-0.2.4}/backend/countmut_expr.c +0 -0
  16. {countmut-0.2.3 → countmut-0.2.4}/backend/countmut_expr.h +0 -0
  17. {countmut-0.2.3 → countmut-0.2.4}/backend/faidx.c +0 -0
  18. {countmut-0.2.3 → countmut-0.2.4}/backend/faidx.h +0 -0
  19. {countmut-0.2.3 → countmut-0.2.4}/backend/hts.c +0 -0
  20. {countmut-0.2.3 → countmut-0.2.4}/backend/hts.h +0 -0
  21. {countmut-0.2.3 → countmut-0.2.4}/backend/ketopt.h +0 -0
  22. {countmut-0.2.3 → countmut-0.2.4}/backend/khash.h +0 -0
  23. {countmut-0.2.3 → countmut-0.2.4}/backend/kseq.h +0 -0
  24. {countmut-0.2.3 → countmut-0.2.4}/backend/ksort.h +0 -0
  25. {countmut-0.2.3 → countmut-0.2.4}/backend/kstdint.h +0 -0
  26. {countmut-0.2.3 → countmut-0.2.4}/backend/kstring.h +0 -0
  27. {countmut-0.2.3 → countmut-0.2.4}/backend/razf.c +0 -0
  28. {countmut-0.2.3 → countmut-0.2.4}/backend/razf.h +0 -0
  29. {countmut-0.2.3 → countmut-0.2.4}/backend/sam.c +0 -0
  30. {countmut-0.2.3 → countmut-0.2.4}/backend/sam.h +0 -0
  31. {countmut-0.2.3 → countmut-0.2.4}/countmut/__init__.py +0 -0
  32. {countmut-0.2.3 → countmut-0.2.4}/countmut/backend.py +0 -0
  33. {countmut-0.2.3 → countmut-0.2.4}/countmut/bam_tags.py +0 -0
  34. {countmut-0.2.3 → countmut-0.2.4}/countmut/cli.py +0 -0
  35. {countmut-0.2.3 → countmut-0.2.4}/countmut/core.py +0 -0
  36. {countmut-0.2.3 → countmut-0.2.4}/countmut/model.py +0 -0
  37. {countmut-0.2.3 → countmut-0.2.4}/countmut/utils.py +0 -0
  38. {countmut-0.2.3 → countmut-0.2.4}/countmut.egg-info/SOURCES.txt +0 -0
  39. {countmut-0.2.3 → countmut-0.2.4}/countmut.egg-info/dependency_links.txt +0 -0
  40. {countmut-0.2.3 → countmut-0.2.4}/countmut.egg-info/entry_points.txt +0 -0
  41. {countmut-0.2.3 → countmut-0.2.4}/countmut.egg-info/requires.txt +0 -0
  42. {countmut-0.2.3 → countmut-0.2.4}/countmut.egg-info/top_level.txt +0 -0
  43. {countmut-0.2.3 → countmut-0.2.4}/setup.cfg +0 -0
  44. {countmut-0.2.3 → countmut-0.2.4}/tests/test_cli.py +0 -0
  45. {countmut-0.2.3 → countmut-0.2.4}/tests/test_core.py +0 -0
  46. {countmut-0.2.3 → countmut-0.2.4}/tests/test_correctness.py +0 -0
  47. {countmut-0.2.3 → countmut-0.2.4}/tests/test_router.py +0 -0
  48. {countmut-0.2.3 → countmut-0.2.4}/tests/test_unified.py +0 -0
  49. {countmut-0.2.3 → countmut-0.2.4}/tests/test_utils.py +0 -0
{countmut-0.2.3/countmut.egg-info → countmut-0.2.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: countmut
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- Version: 0.2.3
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+ Version: 0.2.4
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  Summary: Unified ultra-fast strand-aware mutation counter (C backend + samtools-style -e/-p filters)
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  Author-email: Ye Chang <yech1990@gmail.com>
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  License-Expression: MIT
{countmut-0.2.3 → countmut-0.2.4}/backend/countmut_core_main.c RENAMED
@@ -101,6 +101,7 @@ static int strand_from(const char *s) {
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  int main(int argc, char **argv) {
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  cm_config cfg;
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  memset(&cfg, 0, sizeof(cfg));
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+ cfg.target_base = -1; /* no strand filter by default (--target-base unset) */
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  cfg.out = CM_OUT_COMPOSITION;
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  cfg.engine = CM_ENGINE_AUTO;
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  cfg.min_mapq = 0;
{countmut-0.2.3 → countmut-0.2.4/countmut.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: countmut
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- Version: 0.2.3
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+ Version: 0.2.4
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  Summary: Unified ultra-fast strand-aware mutation counter (C backend + samtools-style -e/-p filters)
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  Author-email: Ye Chang <yech1990@gmail.com>
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  License-Expression: MIT
{countmut-0.2.3 → countmut-0.2.4}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "countmut"
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- version = "0.2.3"
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+ version = "0.2.4"
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  description = "Unified ultra-fast strand-aware mutation counter (C backend + samtools-style -e/-p filters)"
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  readme = "README.md"
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  license = "MIT"
{countmut-0.2.3 → countmut-0.2.4}/LICENSE RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/MANIFEST.in RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/README.md RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/Makefile RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/bedidx.c RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/bgzf.c RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/bgzf.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/faidx.c RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/faidx.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/hts.c RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/hts.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/ketopt.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/khash.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/kseq.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/ksort.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/kstdint.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/kstring.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/razf.c RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/razf.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/sam.c RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/backend/sam.h RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/countmut/__init__.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/countmut/backend.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/countmut/bam_tags.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/countmut/cli.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/countmut/core.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/countmut/model.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/countmut/utils.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/setup.cfg RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/tests/test_cli.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/tests/test_core.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/tests/test_router.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/tests/test_unified.py RENAMED
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{countmut-0.2.3 → countmut-0.2.4}/tests/test_utils.py RENAMED
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