partis-bcr 1.0.12.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12.post1.dev3__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 (51) hide show
  1. packages/bpp/bin/bppseqgen +0 -0
  2. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/METADATA +1 -1
  3. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/RECORD +51 -50
  4. test/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  5. test/new-results/partition-new-simu/fasttree/iclust-1/log +2 -2
  6. test/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  7. test/new-results/run-times.csv +8 -8
  8. test/new-results/test.log +48 -48
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +5 -5
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +5 -5
  11. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  12. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +4 -4
  13. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +4 -4
  14. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +1 -1
  15. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +4 -4
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  31. test/paired/new-results/run-times.csv +6 -6
  32. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +64 -64
  33. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +71 -72
  34. test/paired/new-results/subset-partition-new-simu/merged-partition.log +39 -39
  35. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  36. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  37. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  38. test/paired/new-results/test.log +148 -148
  39. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  40. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  41. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  42. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  43. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/gctree-run.py +0 -0
  44. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  45. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/parse-output.py +0 -0
  46. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/partis-test.py +0 -0
  47. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/split-loci.py +0 -0
  48. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/WHEEL +0 -0
  49. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/entry_points.txt +0 -0
  50. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/licenses/COPYING +0 -0
  51. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/top_level.txt +0 -0
test/paired/new-results/partition-new-simu/fasttree/iclust-2/log CHANGED
@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
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  Rate categories were divided by 0.641 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 = -1274.638 NNIs 0 max delta 0.00 Time 0.03
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+ ML-NNI round 2: LogLk = -1274.638 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 = -1274.638 NNIs 0 max delta 0.00 Time 0.04 (final)
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- Optimize all lengths: LogLk = -1274.638 Time 0.04
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- Total time: 0.06 seconds Unique: 6/6 Bad splits: 0/3
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+ ML-NNI round 3: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.03 (final)
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+ Optimize all lengths: LogLk = -1274.638 Time 0.03
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+ Total time: 0.04 seconds Unique: 6/6 Bad splits: 0/3
test/paired/new-results/partition-new-simu/igh+igk/partition-igh/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 0.678 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 = -968.458 NNIs 0 max delta 0.00 Time 0.03
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+ ML-NNI round 2: LogLk = -968.458 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 = -968.419 NNIs 0 max delta 0.00 Time 0.04 (final)
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- Optimize all lengths: LogLk = -968.417 Time 0.04
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- Total time: 0.05 seconds Unique: 8/8 Bad splits: 0/5
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+ ML-NNI round 3: LogLk = -968.419 NNIs 0 max delta 0.00 Time 0.03 (final)
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+ Optimize all lengths: LogLk = -968.417 Time 0.03
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+ Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5
test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log CHANGED
@@ -9,7 +9,7 @@ Ignored unknown character X (seen 21 times)
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  Initial topology in 0.00 seconds
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  Refining topology: 11 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
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  Total branch-length 0.133 after 0.00 sec
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- ML-NNI round 1: LogLk = -824.130 NNIs 0 max delta 0.00 Time 0.01
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+ ML-NNI round 1: LogLk = -824.130 NNIs 0 max delta 0.00 Time 0.00
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  GTR Frequencies: 0.2278 0.2456 0.3207 0.2059
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  GTR rates(ac ag at cg ct gt) 1.1354 1.3036 0.8502 1.1285 0.5919 1.0000
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  Switched to using 20 rate categories (CAT approximation)
@@ -18,6 +18,6 @@ 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 = -794.353 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 = -794.321 NNIs 0 max delta 0.00 Time 0.03 (final)
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- Optimize all lengths: LogLk = -794.321 Time 0.03
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- Total time: 0.04 seconds Unique: 7/7 Bad splits: 0/4
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+ ML-NNI round 3: LogLk = -794.321 NNIs 0 max delta 0.00 Time 0.02 (final)
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+ Optimize all lengths: LogLk = -794.321 Time 0.02
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+ Total time: 0.03 seconds Unique: 7/7 Bad splits: 0/4
test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log CHANGED
@@ -19,4 +19,4 @@ ML-NNI round 2: LogLk = -1077.707 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 = -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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+ Total time: 0.04 seconds Unique: 9/9 Bad splits: 0/6
test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log CHANGED
@@ -8,7 +8,7 @@ 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: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
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  Total branch-length 0.074 after 0.00 sec
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- ML-NNI round 1: LogLk = -630.173 NNIs 0 max delta 0.00 Time 0.01
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+ ML-NNI round 1: LogLk = -630.173 NNIs 0 max delta 0.00 Time 0.00
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  GTR Frequencies: 0.2044 0.3132 0.2728 0.2096
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  GTR rates(ac ag at cg ct gt) 0.8954 1.2357 1.0576 0.3959 0.3435 1.0000
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  Switched to using 20 rate categories (CAT approximation)
@@ -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