loqusdb 2.7.4__tar.gz → 2.7.7__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 (102) hide show
  1. {loqusdb-2.7.4 → loqusdb-2.7.7}/CHANGELOG.md +9 -0
  2. {loqusdb-2.7.4 → loqusdb-2.7.7}/PKG-INFO +1 -1
  3. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/__init__.py +4 -1
  4. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb.egg-info/PKG-INFO +1 -1
  5. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb.egg-info/requires.txt +1 -1
  6. {loqusdb-2.7.4 → loqusdb-2.7.7}/setup.py +1 -1
  7. {loqusdb-2.7.4 → loqusdb-2.7.7}/CONTRIBUTING.md +0 -0
  8. {loqusdb-2.7.4 → loqusdb-2.7.7}/LICENSE +0 -0
  9. {loqusdb-2.7.4 → loqusdb-2.7.7}/MANIFEST.in +0 -0
  10. {loqusdb-2.7.4 → loqusdb-2.7.7}/README.md +0 -0
  11. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/__main__.py +0 -0
  12. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/build_models/__init__.py +0 -0
  13. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/build_models/case.py +0 -0
  14. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/build_models/profile_variant.py +0 -0
  15. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/build_models/variant.py +0 -0
  16. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/__init__.py +0 -0
  17. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/annotate.py +0 -0
  18. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/cli.py +0 -0
  19. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/delete.py +0 -0
  20. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/export.py +0 -0
  21. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/identity.py +0 -0
  22. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/load.py +0 -0
  23. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/load_profile.py +0 -0
  24. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/migrate.py +0 -0
  25. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/restore.py +0 -0
  26. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/update.py +0 -0
  27. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/view.py +0 -0
  28. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/wipe.py +0 -0
  29. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/constants/__init__.py +0 -0
  30. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/exceptions/__init__.py +0 -0
  31. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/exceptions/case.py +0 -0
  32. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/exceptions/profile.py +0 -0
  33. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/exceptions/vcf.py +0 -0
  34. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/log.py +0 -0
  35. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/models/__init__.py +0 -0
  36. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/models/case.py +0 -0
  37. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/models/identity.py +0 -0
  38. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/models/profile_variant.py +0 -0
  39. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/models/variant.py +0 -0
  40. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/plugins/__init__.py +0 -0
  41. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/plugins/mongo/__init__.py +0 -0
  42. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/plugins/mongo/adapter.py +0 -0
  43. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/plugins/mongo/case.py +0 -0
  44. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/plugins/mongo/profile_variant.py +0 -0
  45. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/plugins/mongo/structural_variant.py +0 -0
  46. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/plugins/mongo/variant.py +0 -0
  47. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/resources/__init__.py +0 -0
  48. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/__init__.py +0 -0
  49. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/annotate.py +0 -0
  50. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/case.py +0 -0
  51. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/delete.py +0 -0
  52. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/load.py +0 -0
  53. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/migrate.py +0 -0
  54. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/profiling.py +0 -0
  55. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/update.py +0 -0
  56. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/variant.py +0 -0
  57. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/vcf.py +0 -0
  58. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb.egg-info/SOURCES.txt +0 -0
  59. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb.egg-info/dependency_links.txt +0 -0
  60. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb.egg-info/entry_points.txt +0 -0
  61. {loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb.egg-info/top_level.txt +0 -0
  62. {loqusdb-2.7.4 → loqusdb-2.7.7}/setup.cfg +0 -0
  63. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/build_models/test_build_case.py +0 -0
  64. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/build_models/test_build_variant.py +0 -0
  65. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/build_models/test_is_greater.py +0 -0
  66. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/commands/test_export.py +0 -0
  67. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/commands/test_identity.py +0 -0
  68. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/commands/test_view.py +0 -0
  69. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/conftest.py +0 -0
  70. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/643594.clinical.SV.vcf +0 -0
  71. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/643594.clinical.vcf.gz +0 -0
  72. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/double_variant.vcf +0 -0
  73. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/funny_trio.ped +0 -0
  74. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/profile_snv.vcf +0 -0
  75. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/recessive_trio.ped +0 -0
  76. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/test.SV.vcf +0 -0
  77. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/test.vcf +0 -0
  78. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/test.vcf.gz +0 -0
  79. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/test.vcf.gz.tbi +0 -0
  80. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/unsorted.vcf +0 -0
  81. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/functional/test_cli.py +0 -0
  82. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/plugins/mongo/test_case_operations.py +0 -0
  83. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/plugins/mongo/test_connect.py +0 -0
  84. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/plugins/mongo/test_flask_extension.py +0 -0
  85. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/plugins/mongo/test_get_sv.py +0 -0
  86. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/plugins/mongo/test_load_svs.py +0 -0
  87. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/plugins/mongo/test_variant_operations.py +0 -0
  88. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/utils/test_case.py +0 -0
  89. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/utils/test_delete.py +0 -0
  90. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/utils/test_delete_family.py +0 -0
  91. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/utils/test_delete_variant.py +0 -0
  92. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/utils/test_get_family.py +0 -0
  93. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/utils/test_load_database.py +0 -0
  94. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/utils/test_load_family.py +0 -0
  95. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/utils/test_load_variants.py +0 -0
  96. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/utils/test_migrate.py +0 -0
  97. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/utils/test_profiling.py +0 -0
  98. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/vcf_tools/test_check_par.py +0 -0
  99. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/vcf_tools/test_check_vcf.py +0 -0
  100. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/vcf_tools/test_format_sv_variant.py +0 -0
  101. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/vcf_tools/test_format_variant.py +0 -0
  102. {loqusdb-2.7.4 → loqusdb-2.7.7}/tests/vcf_tools/test_vcf.py +0 -0
{loqusdb-2.7.4 → loqusdb-2.7.7}/CHANGELOG.md RENAMED
@@ -3,6 +3,15 @@ All notable changes to this project will be documented in this file.
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  This project adheres to [Semantic Versioning](http://semver.org/).
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  About changelog [here](https://keepachangelog.com/en/1.0.0/)
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+
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+ ## [2.7.7]
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+ ### Fixed
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+ - Update to setuptools >= v.70 to address a security issue in the `package_index` module
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+
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+ ## [2.7.6]
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+ ### Fixed
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+ - Updated issue templates
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+
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  ## [2.7.4]
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  ## Changed
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  - When using QUAL values, treat . as 0 quality
{loqusdb-2.7.4 → loqusdb-2.7.7}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: loqusdb
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- Version: 2.7.4
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+ Version: 2.7.7
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  Summary: Store observations of vcf variants in a mongodb
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  Home-page: https://github.com/moonso/loqusdb
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  Author: Måns Magnusson
{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/__init__.py RENAMED
@@ -28,12 +28,14 @@ INDEXES = {
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  "structural_variant": [
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  IndexModel(
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  [
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+ ("sv_type", ASCENDING),
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  ("chrom", ASCENDING),
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  ("end_chrom", ASCENDING),
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- ("sv_type", ASCENDING),
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  ("pos_left", ASCENDING),
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+ ("pos_right", ASCENDING),
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  ],
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  name="coordinates",
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+ background=True,
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  ),
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  IndexModel(
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  [
@@ -42,6 +44,7 @@ INDEXES = {
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  ("end_right", ASCENDING),
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  ],
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  name="short_coordinates",
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+ background=True,
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  ),
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  ],
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  "identity": [
{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: loqusdb
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- Version: 2.7.4
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+ Version: 2.7.7
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  Summary: Store observations of vcf variants in a mongodb
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  Home-page: https://github.com/moonso/loqusdb
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  Author: Måns Magnusson
{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb.egg-info/requires.txt RENAMED
@@ -8,6 +8,6 @@ coloredlogs==14.0
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  pyyaml>=5.4.1
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  vcftoolbox==1.5
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  pip==23.1.2
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- setuptools==65.5.1
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+ setuptools>=70.0.0
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  mongo_adapter
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  ped_parser
{loqusdb-2.7.4 → loqusdb-2.7.7}/setup.py RENAMED
@@ -19,7 +19,7 @@ URL = "https://github.com/moonso/loqusdb"
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  EMAIL = "mans.magnusson@scilifelab.com"
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  AUTHOR = "Måns Magnusson"
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  REQUIRES_PYTHON = ">=3.7.0"
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- VERSION = "2.7.4"
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+ VERSION = "2.7.7"
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  with open('requirements.txt') as f:
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  install_requires = f.read().strip().split('\n')
{loqusdb-2.7.4 → loqusdb-2.7.7}/CONTRIBUTING.md RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/LICENSE RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/MANIFEST.in RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/README.md RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/__main__.py RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/commands/cli.py RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/log.py RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/models/case.py RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/case.py RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/delete.py RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/load.py RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/update.py RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/loqusdb/utils/vcf.py RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/setup.cfg RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/tests/conftest.py RENAMED
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{loqusdb-2.7.4 → loqusdb-2.7.7}/tests/fixtures/test.vcf RENAMED
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