partis-bcr 1.0.13__cp312-cp312-macosx_10_13_universal2.whl → 1.0.13.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 (51) hide show
  1. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/RECORD +51 -51
  3. python/processargs.py +4 -1
  4. test/new-results/partition-new-simu/fasttree/iclust-0/log +5 -5
  5. test/new-results/partition-new-simu/fasttree/iclust-1/log +3 -3
  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 +52 -52
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +2 -2
  11. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +2 -2
  12. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +6 -6
  13. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +1 -1
  14. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +3 -3
  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 +108 -108
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +84 -84
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +62 -62
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +19 -19
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +25 -25
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +36 -36
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +23 -23
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +46 -46
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +46 -46
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +46 -46
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +16 -16
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +16 -16
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +48 -48
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +49 -49
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +28 -28
  31. test/paired/new-results/run-times.csv +6 -6
  32. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +51 -55
  33. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +51 -55
  34. test/paired/new-results/subset-partition-new-simu/merged-partition.log +37 -41
  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 +146 -155
  39. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/cf-alleles.py +0 -0
  40. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/cf-germlines.py +0 -0
  41. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/compare-plotdirs.py +0 -0
  42. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/extract-pairing-info.py +0 -0
  43. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/gctree-run.py +0 -0
  44. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/get-naive-probabilities.py +0 -0
  45. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/parse-output.py +0 -0
  46. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/partis-test.py +0 -0
  47. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/split-loci.py +0 -0
  48. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/WHEEL +0 -0
  49. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/entry_points.txt +0 -0
  50. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/licenses/COPYING +0 -0
  51. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/top_level.txt +0 -0
test/paired/new-results/partition-new-simu/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 0.666 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 = -1660.926 NNIs 0 max delta 0.00 Time 0.06
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+ ML-NNI round 2: LogLk = -1660.926 NNIs 0 max delta 0.00 Time 0.04
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  Turning off heuristics for final round of ML NNIs (converged)
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- ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.08 (final)
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- Optimize all lengths: LogLk = -1660.925 Time 0.08
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- Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5
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+ ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.05 (final)
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+ Optimize all lengths: LogLk = -1660.925 Time 0.05
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+ Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5
test/paired/new-results/partition-new-simu/fasttree/iclust-1/log CHANGED
@@ -19,5 +19,5 @@ Use -gamma for approximate but comparable Gamma(20) log-likelihoods
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  ML-NNI round 2: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.04
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  Turning off heuristics for final round of ML NNIs (converged)
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  ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.05 (final)
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- Optimize all lengths: LogLk = -1478.012 Time 0.06
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- Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5
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+ Optimize all lengths: LogLk = -1478.012 Time 0.05
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+ Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5
test/paired/new-results/partition-new-simu/fasttree/iclust-2/log CHANGED
@@ -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 = -1274.638 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 = -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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+ 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: 0.05 seconds Unique: 6/6 Bad splits: 0/3
test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log CHANGED
@@ -8,16 +8,16 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
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  Ignored unknown character X (seen 24 times)
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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 0.217 after 0.00 sec
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- ML-NNI round 1: LogLk = -1009.286 NNIs 0 max delta 0.00 Time 0.01
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+ Total branch-length 0.217 after 0.01 sec
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+ ML-NNI round 1: LogLk = -1009.286 NNIs 0 max delta 0.00 Time 0.02
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  GTR Frequencies: 0.2219 0.2395 0.3219 0.2167
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  GTR rates(ac ag at cg ct gt) 0.9477 0.4171 1.2893 0.8129 0.9896 1.0000
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  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 0.04
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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 0.03 (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 0.05 (final)
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+ Optimize all lengths: LogLk = -968.417 Time 0.05
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+ Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5
test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log CHANGED
@@ -19,5 +19,5 @@ 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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  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 0.01
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+ Optimize all lengths: LogLk = -457.145 Time 0.00
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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
@@ -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 = -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 0.04 (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
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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
test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log CHANGED
@@ -15,8 +15,8 @@ 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 = -613.260 NNIs 0 max delta 0.00 Time 0.03
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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