partis-bcr 1.0.12.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12.post1.dev4__cp312-cp312-macosx_10_13_universal2.whl

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 (62) hide show
  1. packages/bpp/bin/bppseqgen +0 -0
  2. packages/bpp/lib/libbpp-core.a +0 -0
  3. packages/bpp/lib/libbpp-core.so +0 -0
  4. packages/bpp/lib/libbpp-core.so.2 +0 -0
  5. packages/bpp/lib/libbpp-core.so.2.0.3 +0 -0
  6. packages/bpp/lib/libbpp-phyl.a +0 -0
  7. packages/bpp/lib/libbpp-phyl.so +0 -0
  8. packages/bpp/lib/libbpp-phyl.so.9 +0 -0
  9. packages/bpp/lib/libbpp-phyl.so.9.1.3 +0 -0
  10. packages/bpp/lib/libbpp-seq.a +0 -0
  11. packages/bpp/lib/libbpp-seq.so +0 -0
  12. packages/bpp/lib/libbpp-seq.so.9 +0 -0
  13. packages/bpp/lib/libbpp-seq.so.9.1.3 +0 -0
  14. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/METADATA +1 -1
  15. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/RECORD +62 -49
  16. test/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  17. test/new-results/partition-new-simu/fasttree/iclust-1/log +1 -1
  18. test/new-results/partition-new-simu/fasttree/iclust-2/log +3 -3
  19. test/new-results/run-times.csv +8 -8
  20. test/new-results/test.log +39 -39
  21. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +1 -1
  22. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +1 -1
  23. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +2 -2
  24. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +3 -3
  25. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +5 -5
  26. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +3 -3
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  31. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  32. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  33. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  34. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  35. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  36. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  37. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  38. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  39. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  40. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  41. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  42. test/paired/new-results/run-times.csv +6 -6
  43. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +55 -55
  44. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +55 -55
  45. test/paired/new-results/subset-partition-new-simu/merged-partition.log +29 -29
  46. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  47. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  48. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  49. test/paired/new-results/test.log +128 -128
  50. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/cf-alleles.py +0 -0
  51. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/cf-germlines.py +0 -0
  52. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/compare-plotdirs.py +0 -0
  53. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/extract-pairing-info.py +0 -0
  54. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/gctree-run.py +0 -0
  55. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/get-naive-probabilities.py +0 -0
  56. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/parse-output.py +0 -0
  57. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/partis-test.py +0 -0
  58. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/split-loci.py +0 -0
  59. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/WHEEL +0 -0
  60. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/entry_points.txt +0 -0
  61. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/licenses/COPYING +0 -0
  62. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/top_level.txt +0 -0
test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log CHANGED
@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
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  Rate categories were divided by 0.624 so that average rate = 1.0
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  CAT-based log-likelihoods may not be comparable across runs
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  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
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- ML-NNI round 2: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.00
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+ ML-NNI round 2: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.01
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  Turning off heuristics for final round of ML NNIs (converged)
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- ML-NNI round 3: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.00 (final)
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- Optimize all lengths: LogLk = -457.145 Time 0.00
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+ ML-NNI round 3: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.01 (final)
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+ Optimize all lengths: LogLk = -457.145 Time 0.01
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  Total time: 0.01 seconds Unique: 3/8 Bad splits: 0/0
test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log CHANGED
@@ -7,7 +7,7 @@ TopHits: 1.00*sqrtN close=default refresh=0.80
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  ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
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  Initial topology in 0.00 seconds
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  Refining topology: 13 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
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- Total branch-length 0.284 after 0.00 sec
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+ Total branch-length 0.284 after 0.01 sec
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  ML-NNI round 1: LogLk = -1122.563 NNIs 0 max delta 0.00 Time 0.01
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  GTR Frequencies: 0.2140 0.2925 0.2783 0.2152
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  GTR rates(ac ag at cg ct gt) 1.3956 1.1142 1.5463 0.9911 1.2525 1.0000
@@ -15,8 +15,8 @@ Switched to using 20 rate categories (CAT approximation)
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  Rate categories were divided by 0.695 so that average rate = 1.0
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  CAT-based log-likelihoods may not be comparable across runs
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  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
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- ML-NNI round 2: LogLk = -1077.707 NNIs 0 max delta 0.00 Time 0.02
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+ ML-NNI round 2: LogLk = -1077.707 NNIs 0 max delta 0.00 Time 0.03
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  Turning off heuristics for final round of ML NNIs (converged)
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- ML-NNI round 3: LogLk = -1077.702 NNIs 0 max delta 0.00 Time 0.03 (final)
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- Optimize all lengths: LogLk = -1077.702 Time 0.03
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- Total time: 0.05 seconds Unique: 9/9 Bad splits: 0/6
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+ ML-NNI round 3: LogLk = -1077.702 NNIs 0 max delta 0.00 Time 0.04 (final)
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+ Optimize all lengths: LogLk = -1077.702 Time 0.04
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+ Total time: 0.06 seconds Unique: 9/9 Bad splits: 0/6
test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log CHANGED
@@ -17,6 +17,6 @@ CAT-based log-likelihoods may not be comparable across runs
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  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
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  ML-NNI round 2: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.02
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  Turning off heuristics for final round of ML NNIs (converged)
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- ML-NNI round 3: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.03 (final)
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- Optimize all lengths: LogLk = -613.260 Time 0.03
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- Total time: 0.04 seconds Unique: 8/9 Bad splits: 0/5
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+ ML-NNI round 3: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.02 (final)
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+ Optimize all lengths: LogLk = -613.260 Time 0.02
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+ Total time: 0.03 seconds Unique: 8/9 Bad splits: 0/5