strkit 0.11.5__tar.gz → 0.11.7__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 (59) hide show
  1. {strkit-0.11.5/strkit.egg-info → strkit-0.11.7}/PKG-INFO +1 -1
  2. strkit-0.11.7/strkit/VERSION +1 -0
  3. {strkit-0.11.5 → strkit-0.11.7}/strkit/mi/result.py +7 -3
  4. {strkit-0.11.5 → strkit-0.11.7/strkit.egg-info}/PKG-INFO +1 -1
  5. strkit-0.11.5/strkit/VERSION +0 -1
  6. {strkit-0.11.5 → strkit-0.11.7}/LICENSE +0 -0
  7. {strkit-0.11.5 → strkit-0.11.7}/MANIFEST.in +0 -0
  8. {strkit-0.11.5 → strkit-0.11.7}/README.md +0 -0
  9. {strkit-0.11.5 → strkit-0.11.7}/pyproject.toml +0 -0
  10. {strkit-0.11.5 → strkit-0.11.7}/setup.cfg +0 -0
  11. {strkit-0.11.5 → strkit-0.11.7}/setup.py +0 -0
  12. {strkit-0.11.5 → strkit-0.11.7}/strkit/__init__.py +0 -0
  13. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/__init__.py +0 -0
  14. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/align_matrix.py +0 -0
  15. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/allele.py +0 -0
  16. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/call_locus.py +0 -0
  17. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/call_sample.py +0 -0
  18. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/cigar.py +0 -0
  19. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/non_daemonic_pool.py +0 -0
  20. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/realign.py +0 -0
  21. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/repeats.py +0 -0
  22. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/snvs.py +0 -0
  23. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/types.py +0 -0
  24. {strkit-0.11.5 → strkit-0.11.7}/strkit/call/utils.py +0 -0
  25. {strkit-0.11.5 → strkit-0.11.7}/strkit/catalog/__init__.py +0 -0
  26. {strkit-0.11.5 → strkit-0.11.7}/strkit/catalog/combine.py +0 -0
  27. {strkit-0.11.5 → strkit-0.11.7}/strkit/constants.py +0 -0
  28. {strkit-0.11.5 → strkit-0.11.7}/strkit/convert/__init__.py +0 -0
  29. {strkit-0.11.5 → strkit-0.11.7}/strkit/convert/_bed_4.py +0 -0
  30. {strkit-0.11.5 → strkit-0.11.7}/strkit/convert/converter.py +0 -0
  31. {strkit-0.11.5 → strkit-0.11.7}/strkit/convert/expansionhunter.py +0 -0
  32. {strkit-0.11.5 → strkit-0.11.7}/strkit/convert/gangstr.py +0 -0
  33. {strkit-0.11.5 → strkit-0.11.7}/strkit/convert/hipstr.py +0 -0
  34. {strkit-0.11.5 → strkit-0.11.7}/strkit/convert/straglr.py +0 -0
  35. {strkit-0.11.5 → strkit-0.11.7}/strkit/convert/tandem_genotypes.py +0 -0
  36. {strkit-0.11.5 → strkit-0.11.7}/strkit/entry.py +0 -0
  37. {strkit-0.11.5 → strkit-0.11.7}/strkit/exceptions.py +0 -0
  38. {strkit-0.11.5 → strkit-0.11.7}/strkit/json.py +0 -0
  39. {strkit-0.11.5 → strkit-0.11.7}/strkit/logger.py +0 -0
  40. {strkit-0.11.5 → strkit-0.11.7}/strkit/mi/__init__.py +0 -0
  41. {strkit-0.11.5 → strkit-0.11.7}/strkit/mi/base.py +0 -0
  42. {strkit-0.11.5 → strkit-0.11.7}/strkit/mi/expansionhunter.py +0 -0
  43. {strkit-0.11.5 → strkit-0.11.7}/strkit/mi/gangstr.py +0 -0
  44. {strkit-0.11.5 → strkit-0.11.7}/strkit/mi/repeathmm.py +0 -0
  45. {strkit-0.11.5 → strkit-0.11.7}/strkit/mi/straglr.py +0 -0
  46. {strkit-0.11.5 → strkit-0.11.7}/strkit/mi/strkit.py +0 -0
  47. {strkit-0.11.5 → strkit-0.11.7}/strkit/mi/tandem_genotypes.py +0 -0
  48. {strkit-0.11.5 → strkit-0.11.7}/strkit/mi/vcf_utils.py +0 -0
  49. {strkit-0.11.5 → strkit-0.11.7}/strkit/utils.py +0 -0
  50. {strkit-0.11.5 → strkit-0.11.7}/strkit/viz/__init__.py +0 -0
  51. {strkit-0.11.5 → strkit-0.11.7}/strkit/viz/server.py +0 -0
  52. {strkit-0.11.5 → strkit-0.11.7}/strkit/viz/static/logo.png +0 -0
  53. {strkit-0.11.5 → strkit-0.11.7}/strkit/viz/templates/browser.html +0 -0
  54. {strkit-0.11.5 → strkit-0.11.7}/strkit.egg-info/SOURCES.txt +0 -0
  55. {strkit-0.11.5 → strkit-0.11.7}/strkit.egg-info/dependency_links.txt +0 -0
  56. {strkit-0.11.5 → strkit-0.11.7}/strkit.egg-info/entry_points.txt +0 -0
  57. {strkit-0.11.5 → strkit-0.11.7}/strkit.egg-info/requires.txt +0 -0
  58. {strkit-0.11.5 → strkit-0.11.7}/strkit.egg-info/top_level.txt +0 -0
  59. {strkit-0.11.5 → strkit-0.11.7}/tests/test_caller_utils.py +0 -0
{strkit-0.11.5/strkit.egg-info → strkit-0.11.7}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: strkit
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- Version: 0.11.5
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+ Version: 0.11.7
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  Summary: A toolkit for analyzing variation in short(ish) tandem repeats.
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  Home-page: https://github.com/davidlougheed/strkit
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  Author: David Lougheed
strkit-0.11.7/strkit/VERSION ADDED
@@ -0,0 +1 @@
1
+ 0.11.7
{strkit-0.11.5 → strkit-0.11.7}/strkit/mi/result.py RENAMED
@@ -212,8 +212,12 @@ class MILocusData:
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  ))
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  def _respects_mi_ci(self, c_gt_ci, m_gt_ci, f_gt_ci, widen: float) -> Optional[bool]:
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- if any(x is None for x in (c_gt_ci, m_gt_ci, f_gt_ci)):
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- return None
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+ for x in (c_gt_ci, m_gt_ci, f_gt_ci):
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+ if x is None:
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+ return None
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+ for y in x:
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+ if y is None:
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+ return None
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  try:
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  m_gt_ci_0 = (m_gt_ci[0][0] - (m_gt_ci[0][0] * widen), m_gt_ci[0][1] + (m_gt_ci[0][1] * widen))
@@ -667,7 +671,7 @@ class MIResult:
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671
 
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  for i in range(len(bins)):
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  vsb = vals_strict_by_bin[i]
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- vpm1b = vals_strict_by_bin[i]
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+ vpm1b = vals_pm1_by_bin[i]
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  v95b = vals_95_ci_by_bin[i] if vals_95_ci_by_bin else None
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  v99b = vals_99_ci_by_bin[i] if vals_95_ci_by_bin else None
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{strkit-0.11.5 → strkit-0.11.7/strkit.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: strkit
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- Version: 0.11.5
3
+ Version: 0.11.7
4
4
  Summary: A toolkit for analyzing variation in short(ish) tandem repeats.
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5
  Home-page: https://github.com/davidlougheed/strkit
6
6
  Author: David Lougheed
strkit-0.11.5/strkit/VERSION DELETED
@@ -1 +0,0 @@
1
- 0.11.5
{strkit-0.11.5 → strkit-0.11.7}/LICENSE RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/MANIFEST.in RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/README.md RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/pyproject.toml RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/setup.cfg RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/setup.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/__init__.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/call/__init__.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/call/allele.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/call/cigar.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/call/realign.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/call/repeats.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/call/snvs.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/call/types.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/call/utils.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/constants.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/entry.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/exceptions.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/json.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/logger.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/mi/__init__.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/mi/base.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/mi/gangstr.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/mi/repeathmm.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/mi/straglr.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/mi/strkit.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/mi/vcf_utils.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/utils.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/viz/__init__.py RENAMED
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{strkit-0.11.5 → strkit-0.11.7}/strkit/viz/server.py RENAMED
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