partis-bcr 1.0.12.post1.dev3__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 (63) hide show
  1. packages/bpp/lib/libbpp-core.a +0 -0
  2. packages/bpp/lib/libbpp-core.so +0 -0
  3. packages/bpp/lib/libbpp-core.so.2 +0 -0
  4. packages/bpp/lib/libbpp-core.so.2.0.3 +0 -0
  5. packages/bpp/lib/libbpp-phyl.a +0 -0
  6. packages/bpp/lib/libbpp-phyl.so +0 -0
  7. packages/bpp/lib/libbpp-phyl.so.9 +0 -0
  8. packages/bpp/lib/libbpp-phyl.so.9.1.3 +0 -0
  9. packages/bpp/lib/libbpp-seq.a +0 -0
  10. packages/bpp/lib/libbpp-seq.so +0 -0
  11. packages/bpp/lib/libbpp-seq.so.9 +0 -0
  12. packages/bpp/lib/libbpp-seq.so.9.1.3 +0 -0
  13. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/METADATA +1 -1
  14. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/RECORD +63 -51
  15. test/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  16. test/new-results/partition-new-simu/fasttree/iclust-1/log +3 -3
  17. test/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  18. test/new-results/run-times.csv +8 -8
  19. test/new-results/test.log +45 -45
  20. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +5 -5
  21. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +6 -6
  22. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  23. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +5 -5
  24. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +4 -4
  25. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +3 -3
  26. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +5 -5
  27. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +1 -1
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  31. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  32. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  33. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  34. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  35. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  36. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  37. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  38. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  39. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  40. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  41. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  42. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  43. test/paired/new-results/run-times.csv +6 -6
  44. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +68 -68
  45. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +71 -70
  46. test/paired/new-results/subset-partition-new-simu/merged-partition.log +37 -37
  47. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  48. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  49. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  50. test/paired/new-results/test.log +146 -146
  51. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/cf-alleles.py +0 -0
  52. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/cf-germlines.py +0 -0
  53. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/compare-plotdirs.py +0 -0
  54. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/extract-pairing-info.py +0 -0
  55. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/gctree-run.py +0 -0
  56. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/get-naive-probabilities.py +0 -0
  57. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/parse-output.py +0 -0
  58. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/partis-test.py +0 -0
  59. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/split-loci.py +0 -0
  60. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/WHEEL +0 -0
  61. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/entry_points.txt +0 -0
  62. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/licenses/COPYING +0 -0
  63. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/top_level.txt +0 -0
test/paired/new-results/partition-new-simu/fasttree/iclust-1/log CHANGED
@@ -8,16 +8,16 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
8
8
  Ignored unknown character X (seen 176 times)
9
9
  Initial topology in 0.00 seconds
10
10
  Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
11
- Total branch-length 0.116 after 0.00 sec
12
- ML-NNI round 1: LogLk = -1516.977 NNIs 0 max delta 0.00 Time 0.01
11
+ Total branch-length 0.116 after 0.01 sec
12
+ ML-NNI round 1: LogLk = -1516.977 NNIs 0 max delta 0.00 Time 0.02
13
13
  GTR Frequencies: 0.2498 0.2482 0.2788 0.2231
14
14
  GTR rates(ac ag at cg ct gt) 0.7182 0.4393 0.9759 0.8068 0.8119 1.0000
15
15
  Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.652 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.03
19
+ ML-NNI round 2: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.05
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.04 (final)
22
- Optimize all lengths: LogLk = -1478.012 Time 0.04
23
- Total time: 0.06 seconds Unique: 8/8 Bad splits: 0/5
21
+ ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.06 (final)
22
+ Optimize all lengths: LogLk = -1478.012 Time 0.06
23
+ Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5
test/paired/new-results/partition-new-simu/fasttree/iclust-2/log CHANGED
@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.641 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.02
19
+ ML-NNI round 2: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.03
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.03 (final)
22
- Optimize all lengths: LogLk = -1274.638 Time 0.03
23
- Total time: 0.04 seconds Unique: 6/6 Bad splits: 0/3
21
+ ML-NNI round 3: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.04 (final)
22
+ Optimize all lengths: LogLk = -1274.638 Time 0.04
23
+ Total time: 0.06 seconds Unique: 6/6 Bad splits: 0/3
test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log CHANGED
@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
8
8
  Ignored unknown character X (seen 24 times)
9
9
  Initial topology in 0.00 seconds
10
10
  Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
11
- Total branch-length 0.217 after 0.00 sec
11
+ Total branch-length 0.217 after 0.01 sec
12
12
  ML-NNI round 1: LogLk = -1009.286 NNIs 0 max delta 0.00 Time 0.01
13
13
  GTR Frequencies: 0.2219 0.2395 0.3219 0.2167
14
14
  GTR rates(ac ag at cg ct gt) 0.9477 0.4171 1.2893 0.8129 0.9896 1.0000
@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.678 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -968.458 NNIs 0 max delta 0.00 Time 0.02
19
+ ML-NNI round 2: LogLk = -968.458 NNIs 0 max delta 0.00 Time 0.03
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -968.419 NNIs 0 max delta 0.00 Time 0.03 (final)
22
- Optimize all lengths: LogLk = -968.417 Time 0.03
23
- Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5
21
+ ML-NNI round 3: LogLk = -968.419 NNIs 0 max delta 0.00 Time 0.04 (final)
22
+ Optimize all lengths: LogLk = -968.417 Time 0.04
23
+ Total time: 0.06 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)
9
9
  Initial topology in 0.00 seconds
10
10
  Refining topology: 11 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
11
11
  Total branch-length 0.133 after 0.00 sec
12
- ML-NNI round 1: LogLk = -824.130 NNIs 0 max delta 0.00 Time 0.00
12
+ ML-NNI round 1: LogLk = -824.130 NNIs 0 max delta 0.00 Time 0.01
13
13
  GTR Frequencies: 0.2278 0.2456 0.3207 0.2059
14
14
  GTR rates(ac ag at cg ct gt) 1.1354 1.3036 0.8502 1.1285 0.5919 1.0000
15
15
  Switched to using 20 rate categories (CAT approximation)
@@ -18,6 +18,6 @@ CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
19
  ML-NNI round 2: LogLk = -794.353 NNIs 0 max delta 0.00 Time 0.02
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -794.321 NNIs 0 max delta 0.00 Time 0.02 (final)
22
- Optimize all lengths: LogLk = -794.321 Time 0.02
23
- Total time: 0.03 seconds Unique: 7/7 Bad splits: 0/4
21
+ ML-NNI round 3: LogLk = -794.321 NNIs 0 max delta 0.00 Time 0.03 (final)
22
+ Optimize all lengths: LogLk = -794.321 Time 0.03
23
+ Total time: 0.04 seconds Unique: 7/7 Bad splits: 0/4
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)
16
16
  Rate categories were divided by 0.624 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.00
19
+ ML-NNI round 2: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.01
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.00 (final)
22
- Optimize all lengths: LogLk = -457.145 Time 0.00
21
+ ML-NNI round 3: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.01 (final)
22
+ Optimize all lengths: LogLk = -457.145 Time 0.01
23
23
  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
7
7
  ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
8
8
  Initial topology in 0.00 seconds
9
9
  Refining topology: 13 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
10
- Total branch-length 0.284 after 0.00 sec
10
+ Total branch-length 0.284 after 0.01 sec
11
11
  ML-NNI round 1: LogLk = -1122.563 NNIs 0 max delta 0.00 Time 0.01
12
12
  GTR Frequencies: 0.2140 0.2925 0.2783 0.2152
13
13
  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)
15
15
  Rate categories were divided by 0.695 so that average rate = 1.0
16
16
  CAT-based log-likelihoods may not be comparable across runs
17
17
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
18
- ML-NNI round 2: LogLk = -1077.707 NNIs 0 max delta 0.00 Time 0.02
18
+ ML-NNI round 2: LogLk = -1077.707 NNIs 0 max delta 0.00 Time 0.03
19
19
  Turning off heuristics for final round of ML NNIs (converged)
20
- ML-NNI round 3: LogLk = -1077.702 NNIs 0 max delta 0.00 Time 0.03 (final)
21
- Optimize all lengths: LogLk = -1077.702 Time 0.03
22
- Total time: 0.04 seconds Unique: 9/9 Bad splits: 0/6
20
+ ML-NNI round 3: LogLk = -1077.702 NNIs 0 max delta 0.00 Time 0.04 (final)
21
+ Optimize all lengths: LogLk = -1077.702 Time 0.04
22
+ 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
@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
8
8
  Initial topology in 0.00 seconds
9
9
  Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
10
10
  Total branch-length 0.074 after 0.00 sec
11
- ML-NNI round 1: LogLk = -630.173 NNIs 0 max delta 0.00 Time 0.00
11
+ ML-NNI round 1: LogLk = -630.173 NNIs 0 max delta 0.00 Time 0.01
12
12
  GTR Frequencies: 0.2044 0.3132 0.2728 0.2096
13
13
  GTR rates(ac ag at cg ct gt) 0.8954 1.2357 1.0576 0.3959 0.3435 1.0000
14
14
  Switched to using 20 rate categories (CAT approximation)