partis-bcr 1.0.12.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.12.post1.dev2__cp312-cp312-manylinux1_x86_64.whl

{partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.12.post1.dev1
+Version: 1.0.12.post1.dev2
 Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
 Home-page: https://github.com/psathyrella/partis
 Author: Duncan Ralph

{partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/RECORD

@@ -301,18 +301,19 @@ data/substitution-profiles/GSSPs_for_VH_genes_with_at_least_300_lineages.txt,sha
 data/substitution-profiles/GSSPs_for_VK_genes_with_at_least_300_lineages.txt,sha256=dyMU1R_Izk_ciOVTNWmGL5SQBIKDCCKpxXM6eTGO4Fg,184138
 data/substitution-profiles/GSSPs_for_VL_genes_with_at_least_300_lineages.txt,sha256=CMFb1gk8MbfaMb6y0_qLLiKErrx866C2EafKRSPesB4,184979
 data/substitution-profiles/notes.txt,sha256=-DK9E31YovqOWaXR1Q-LL5KFhjVJcSLwXbriajUq1TA,389
-packages/ham/bcrham,sha256=1g26DafyE_6wglae2TUXc6xkpd2AUp0LDV6Kl_2S7jY,852320
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 packages/ig-sw/src/ig_align/ig-sw,sha256=lYbqn7wujB6j1T7BGeeCqw5kwbPFn0213lDfUBmJb98,282048
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 python/alleleclusterer.py,sha256=x50E_lJMlKPc-CPkdkM1qe4AvVi-mkDJ1cBDxs5L-ms,30551
 python/allelefinder.py,sha256=SgJjopk5ivLOcmTumsWq5PZ05aPZ6zQyjTd1fxeRjaM,80402
@@ -378,9 +379,9 @@ test/new-results/cache-new-partition.csv,sha256=jHVEFlsBiSpjesVSFycef8WPFOc47b2B
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 test/new-results/vsearch-partition-new-simu.yaml,sha256=8TCi7_M9ozjXkK82q2vdMD4yUgxwmjjORXPJVmrgReY,36290
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@@ -502,13 +503,13 @@ test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_ha
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@@ -974,8 +975,8 @@ test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-4_star_09.csv,sha256
 test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-61_star_01.csv,sha256=kONUU7EHhpBiHqSGDoWdTA5zBjaMYZDo385OHxsD5_w,40111
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@@ -990,20 +991,20 @@ test/paired/new-results/partition-new-simu/true-pair-clean-performance-unpaired.
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.csv,sha256=czqVh4ZxAreW2aCwKTHVad8buECSwn1eKK5RToGuESM,402
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg,sha256=cuxMIUg6aTpDSGQ_fFeETzToOQSCer4lTluh_Dlqz3s,12648
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.csv,sha256=1cg0nJL4pkiPxn3jM1c_31pxKPM47KXGZuVp7v-Qz1M,296
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg,sha256=jr_dk-sIpWe8jiBqtBlSInlELkFB5DPP2Z2ZZDmheqY,7249
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.csv,sha256=1cg0nJL4pkiPxn3jM1c_31pxKPM47KXGZuVp7v-Qz1M,296
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.csv,sha256=6H8vsJkv89E5OaepY5bg1DnptEIePK6-C6QjuaBRXv4,337
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg,sha256=SlvaGOlvJPTzPMOONi0b95_vXTuW9uMiZ9aie7lUkxA,13482
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg,sha256=JT85SfSjBhxT3Lhc00ViY1of2AUZnkFjriNlp-NTLUI,13482
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.csv,sha256=tzXelx5oSqhgkstNA-6DGK027GYT-M4TXrFGDEWNEcg,405
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg,sha256=k0rzhbT9pOZZhTEhppu38nphTQFcv9ZU4V_F1CCQ184,13931
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.csv,sha256=EgjeHR05wFVPUvq8acCzf2LhT4c7niHXpEIoc9XyX9Q,178
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=tF86L0W3vNFQswsYmG3FPxvDVAsEcPrim_e3Pt9X58g,9771
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=b3Obx8JFlxL5BkNl8b9L9uB-oN7_X5QtMGLEYp_OZu4,9771
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/d_3p_del.csv,sha256=P0iNxvqMk9z8jTIYcGjxfKa-T2JIi3eOSh3eXPEnBvM,318
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/d_5p_del.csv,sha256=G4CoyPjc1MSkQnVijOv2ysz56zGYG4i-QYelQU-un10,635
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/dj_insertion.csv,sha256=kLzxSn3wfZysDk4IhTlgvEsvdNbLWYOJgMTz_nqRJHU,233
@@ -1250,7 +1251,7 @@ test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igh.yaml,sha256=9Pxnw0p8Ug9ZMVcg7X7RMHURhxpWtpj4h93WuuVS-NY,31446
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igk.yaml,sha256=ZPuU2MYn7BLZmOJ6jUiH-oCa3SaZAr0jVMEAePScKxA,14687
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml,sha256=Ls3u67M8CfP5yaBnfud78p7L9uwH1B0BXGkFwHf48to,6542
-test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=ZBwW-1YIRtCYVGVr4jopbsq9G8YVcmpWpflLbyfCPr0,30272
+test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=h9OMxOhPc_9FxwqcSvLFl9EvR-beb7n--ibH5KSYFks,30272
 test/paired/new-results/subset-partition-new-simu/partition-igh.yaml,sha256=HgoqpG1_ChEuLNouoAGTWOJTKXDR9TP6y_TFxIMmprI,66188
 test/paired/new-results/subset-partition-new-simu/partition-igk.yaml,sha256=Mwg9UfLe-e0sYsvxNgiepogOj0DxuIUECIktiMu_f-A,46690
 test/paired/new-results/subset-partition-new-simu/partition-igl.yaml,sha256=Wi-WCJfj2dWt0E0eSbKaSnY9zajo9lzpZnIVw7mF9OY,19395
@@ -1274,7 +1275,7 @@ test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml,sha256=ZUaFW7
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igh.yaml,sha256=AcC85PCqK8Epm4ICu4B8q5eUjtsmlFTQwTkmMhZqQ5I,30562
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igk.yaml,sha256=TrjOFEnyjqRB1mIbZaG2dDUg0BB7h_YMn7P7NJ4siRA,24486
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igl.yaml,sha256=fc2SzIWy51agwAZcCTJZAfZW_-ddT-g0celyJsbelgY,7960
-test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=JLbJOnwNw6_q_itnpH82XChITvc8CEJpv5SZKUe5_0g,24021
+test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=Fdk9XynQznj5jc5PWzJfWgoALj5Oio9scQ8ieqfVcUs,24021
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/igh.fa,sha256=vR3IfQGVf6SVv6ls-ebrcQmDTDxNu0nhjizzNbitup4,5852
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/igk.fa,sha256=_fxa0GOLuWDb0sfWeO4YbSmIcKwuG4F_4fMxte4dYLE,5107
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh.yaml,sha256=FjL_OaOcNDHHamp3ehFMyAuU4sO4_TMXgEAPlI1kBdw,22125
@@ -1625,7 +1626,7 @@ test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml,sha256=J_IVfe
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igh.yaml,sha256=BiuYTVEBQq5uK6kM1ywk5H5q_ebrK7YJ_38iBuRi2eU,45209
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igk.yaml,sha256=93vPGzB3jaCjPPBEUEvqSqf2axzmd1Ry0P6-YoN7OTg,28793
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igl.yaml,sha256=rzwVZ9JijOgNZAWVW5MaiYTNW6HtQvsrqKPV_y9NT30,14925
-test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=86t5KG65ak8GAyoXLQDqZcgqQawJ6i0impC_fUHki-c,23969
+test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=k5uuRTPouAQbwv3jlS0CyzapzFdsqtuvrOXuKlxtp1Y,23969
 test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/igh.fa,sha256=eLpqTnZF03J8ZANDLzei2lXYLU_qMIPYekhVpRgggfk,8772
 test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/igk.fa,sha256=jWCEqF1B5bXygBLb2BKWKD0rmftFl0c0X5xSEEJOtFA,5868
 test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml,sha256=7OOGwBLiWX7eI9gab1rd3lhRF12WYe7uyrASBEqL7Eg,27612
@@ -1994,7 +1995,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partiti
 test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partition-igk.yaml,sha256=Ybr2uxzr0wzPyEwrxDWDYif2gFk4UlHNPsXmufeFZhg,50990
 test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igl/partition-igh.yaml,sha256=2ip81MiUa7l716-y86dipwvwM3qg1VWlRQT-__6o4Rw,29796
 test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igl/partition-igl.yaml,sha256=dIOx35YYPOx2RQ2e2-Qyac5qegCzHf-DyhML42ZXZIA,21443
-test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=G0YMlBl_kgRFZeJ3NE0JV7cjlOaazzshspd5ZHk0OYA,140753
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=_JtPCF3E6Ew1JV6NcrdxFY7xd1nFt2jwIfHm9HUUUU8,140753
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/all-mean-mute-freqs.csv,sha256=LPJkL33RJZwT1nbvv80p_1r5J6pSyejnAb1rxjB5eU8,912
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/d_gene-probs.csv,sha256=zeYbss9bxXW-xyVRkX6eBeMhPy-qiino5f0xJ5z86DI,233
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/j_gene-probs.csv,sha256=u4L0N-3x-YChG9C2unXpDbDTVzDZgfw3aChq3fHOuSk,63
@@ -2028,7 +2029,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV3-33_star_01.yaml,sha256=FU4oDYBlqRgZwlQrbG23AEZneBh-icKPaswTKnXojUI,103996
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV3-7_star_01.yaml,sha256=GLt0fNZJsArlWs95oE7v2E-ZKciqmRa6plG-AWAxaCg,104240
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV4-39_star_01.yaml,sha256=GGUYeGeP3CaMWhWo4B32FWDF5ohfVAJf8_QwQ9sSkp0,104436
-test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=nNOGw2WN1HpUN8UfzG2gHDyZ701-vPgonuHSYeZMGVM,78754
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=f0loJsctw5awzoh87HV7l6LbV36OKgKBM_W7Vl38VEw,78754
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/all-mean-mute-freqs.csv,sha256=yR5AuVGrcUAOe72bT-nEJap_zn3AwCpaXSrFGELbDyA,740
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/d_gene-probs.csv,sha256=p07NACPyIrtcnGVLP8tHoSHCBiO_H7OazG_siOykHws,28
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/j_gene-probs.csv,sha256=40-_sM8ZQBd6J9r__bewvD1wb3DELCmaRHpLak-xa0s,75
@@ -2047,7 +2048,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV2-30_star_01.yaml,sha256=otPu6N94wuSVkMB8R4ZUYp0k0NLTXBreU1OCCc1VYBk,107159
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV3-11_star_01.yaml,sha256=dizIw0o2xB1DiUzb_HneMaz3yIIyxS0d2HiPCdwo2fA,102590
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV3-15_star_01.yaml,sha256=1z0A-rW4uPkaZ0u-3Vu9fxdBoNqsf8MXfaT6yjkaKxw,103093
-test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=S9Nob7g6UxMMfQegxHar8SRWMeZQjFJonPDUpecvg2A,44439
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=lJ7K3fKovubzGPcOneuQdTc0_mJGqyQT8k1y0GwEGAo,44439
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm/all-mean-mute-freqs.csv,sha256=mhl_3xQduo9KwGA20exKyZmQOOdXC5k5HnFS05ySwb0,693
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm/d_gene-probs.csv,sha256=fJ9zLdtkRjPmYgE7qmoz00lDMlBYXZIvOc-N_WNztlE,28
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm/j_gene-probs.csv,sha256=ng_-k77f0BCTsX-VM_EGVf0CIxPYj59BGGkibFelC60,39
@@ -8426,8 +8427,8 @@ test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV4-NL1_star_01.csv
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV5-10-1_star_01.csv,sha256=S075HCAZnbZpAMsXeLMmMXEGVHFs_Euk1XujtFQ46y4,41974
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv,sha256=QJGyDRqD2JezXsuMbNNXGSCM-kjaN2h4QGpgsaqTqXQ,57817
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV7-4-1_star_02.csv,sha256=k5KeCR5Qa6iEF0IEHR63DDdJStqAjcZxgZOUbKDFNaY,39977
-partis_bcr-1.0.12.post1.dev1.dist-info/METADATA,sha256=JYU6Fwkqn8OYJSp80Fq6ML7ZdYIwgmnTRPiM5MJRUmQ,5019
-partis_bcr-1.0.12.post1.dev1.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
-partis_bcr-1.0.12.post1.dev1.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.12.post1.dev1.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.12.post1.dev1.dist-info/RECORD,,
+partis_bcr-1.0.12.post1.dev2.dist-info/METADATA,sha256=S7BCLjbDeGvZAIOfKGqCVg1S_0r5K1d31Owh4gHLUgA,5019
+partis_bcr-1.0.12.post1.dev2.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
+partis_bcr-1.0.12.post1.dev2.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.12.post1.dev2.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.12.post1.dev2.dist-info/RECORD,,

test/new-results/partition-new-simu/fasttree/iclust-0/log

@@ -18,6 +18,6 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -655.501 NNIs 1 max delta 0.00 Time 0.03
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -655.501 NNIs 1 max delta 0.00 Time 0.03 (final)
-Optimize all lengths: LogLk = -655.501 Time 0.03
-Total time: 0.04 seconds Unique: 8/12 Bad splits: 0/5
+ML-NNI round 3: LogLk = -655.501 NNIs 1 max delta 0.00 Time 0.04 (final)
+Optimize all lengths: LogLk = -655.501 Time 0.04
+Total time: 0.05 seconds Unique: 8/12 Bad splits: 0/5

test/new-results/partition-new-simu/fasttree/iclust-2/log

@@ -17,6 +17,6 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -662.808 NNIs 2 max delta 0.00 Time 0.03
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -662.808 NNIs 1 max delta 0.00 Time 0.03 (final)
+ML-NNI round 3: LogLk = -662.808 NNIs 1 max delta 0.00 Time 0.04 (final)
 Optimize all lengths: LogLk = -662.808 Time 0.04
-Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5
+Total time: 0.05 seconds Unique: 8/8 Bad splits: 0/5

test/new-results/run-times.csv

@@ -1,10 +1,10 @@
 name,seconds
 cache-parameters-simu,5.2
-annotate-new-simu,2.0
-multi-annotate-new-simu,1.8
+annotate-new-simu,2.1
+multi-annotate-new-simu,1.9
 partition-new-simu,3.1
-seed-partition-new-simu,1.6
+seed-partition-new-simu,1.7
 vsearch-partition-new-simu,1.9
 get-selection-metrics-new-simu,1.4
-cache-parameters-data,6.1
-simulate,7.3
+cache-parameters-data,6.2
+simulate,7.4

test/new-results/test.log

@@ -18,7 +18,7 @@ smith-waterman  (writing parameters)
       info for 36 / 36 = 1.000   (removed: 0 failed)
       kept 18 (0.500) unproductive
         writing sw results to test/new-results/test/parameters/simu/sw-cache.yaml
-    writing parameters to test/new-results/test/parameters/simu/sw (0.6 sec)
+    writing parameters to test/new-results/test/parameters/simu/sw (0.7 sec)
     water time: 0.8  (ig-sw 0.7  processing 0.0)
   writing hmms     removed 30 genes from glfo (leaving v 7  d 5  j 3)
 (0.5 sec)
@@ -49,8 +49,8 @@ hmm
   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
-      hmm step time: 0.6
-      total time: 0.7
+      hmm step time: 0.7
+      total time: 0.8
 multi-annotate-new-simu          partis annotate --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --simultaneous-true-clonal-seqs --is-simu --plotdir test/new-results/multi-annotate-new-simu-annotation-performance --only-csv-plots --random-seed 1 --n-procs 10 --outfname test/new-results/multi-annotate-new-simu.yaml
 annotating    (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
@@ -178,7 +178,7 @@ getting annotations for final partition
       warning get_aa_tree() (AA inf tree, iclust 2): skipped 11/13 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: apr dhq fnv nox uvx
     skipped 1/4 clusters that had no uids in common with tree
   writing selection metrics to test/new-results/get-selection-metrics-new-simu.yaml
-      total time: 0.2
+      total time: 0.1
 cache-parameters-data            partis cache-parameters --dont-write-git-info --infname test/mishmash.fa --parameter-dir test/new-results/test/parameters/data --sw-cachefname test/new-results/test/parameters/data/sw-cache.yaml --n-max-queries 50 --input-metafnames test/input-meta.yaml --random-seed 1 --n-procs 10
     stopped after reading 50 sequences from test/mishmash.fa
   --n-max-queries: stopped after reading 50 queries from input file
@@ -201,7 +201,7 @@ smith-waterman  (writing parameters)
       kept 16 (0.320) unproductive
         writing sw results to test/new-results/test/parameters/data/sw-cache.yaml
     writing parameters to test/new-results/test/parameters/data/sw (0.8 sec)
-    water time: 1.0  (ig-sw 0.9  processing 0.0)
+    water time: 0.9  (ig-sw 0.9  processing 0.0)
   writing hmms     removed 15 genes from glfo (leaving v 18  d 22  j 7)
 (0.8 sec)
 hmm
@@ -209,9 +209,9 @@ hmm
         read 46 hmm output lines with 46 sequences in 46 events  (0 failures)
     writing parameters to test/new-results/test/parameters/data/hmm (0.7 sec)
          infra time: 0.8
-      hmm step time: 2.2
+      hmm step time: 2.3
   writing hmms     removed 6  genes from glfo (leaving v 15  d 19  j 7)
-(0.7 sec)
+(0.6 sec)
       total time: 4.9
 simulate                         partis simulate --dont-write-git-info --parameter-dir test/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1 --n-procs 10 --outfname test/new-results/test/simu.yaml --indel-frequency 0.2
 simulating
@@ -219,7 +219,7 @@ simulating
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 6 seqs in 0.1s (0.1s of which was running bppseqgen)
-      total time: 0.2
+      total time: 0.3
 
       --> proc 1
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
@@ -230,25 +230,25 @@ simulating
       --> proc 2
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 2 seqs in 0.2s (0.1s of which was running bppseqgen)
+    made 1 event with 2 seqs in 0.1s (0.1s of which was running bppseqgen)
       total time: 0.3
 
       --> proc 3
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 11 seqs in 0.2s (0.1s of which was running bppseqgen)
-      total time: 0.3
+    made 1 event with 11 seqs in 0.3s (0.1s of which was running bppseqgen)
+      total time: 0.4
 
       --> proc 4
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 4 seqs in 0.2s (0.1s of which was running bppseqgen)
+    made 1 event with 4 seqs in 0.1s (0.1s of which was running bppseqgen)
       total time: 0.3
 
       --> proc 5
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 22 seqs in 0.3s (0.2s of which was running bppseqgen)
+    made 1 event with 22 seqs in 0.3s (0.1s of which was running bppseqgen)
       total time: 0.4
 
       --> proc 6
@@ -261,7 +261,7 @@ simulating
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 3 seqs in 0.1s (0.1s of which was running bppseqgen)
-      total time: 0.2
+      total time: 0.3
 
       --> proc 8
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
@@ -276,4 +276,4 @@ simulating
       total time: 0.3
 
    read 10 events with 74 seqs from 10 .yaml files
-      total time: 6.0
+      total time: 6.1

test/paired/new-results/partition-new-simu/fasttree/iclust-0/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.666 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07
+ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.06
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.08 (final)
-Optimize all lengths: LogLk = -1661.140 Time 0.09
-Total time: 0.11 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07 (final)
+Optimize all lengths: LogLk = -1661.140 Time 0.07
+Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/fasttree/iclust-1/log

@@ -18,6 +18,6 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.07
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.09 (final)
+ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.08 (final)
 Optimize all lengths: LogLk = -1478.012 Time 0.09
 Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/fasttree/iclust-2/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.641 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.04
+ML-NNI round 2: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.05
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.04 (final)
-Optimize all lengths: LogLk = -1274.921 Time 0.05
-Total time: 0.06 seconds Unique: 6/6 Bad splits: 0/3
+ML-NNI round 3: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.06 (final)
+Optimize all lengths: LogLk = -1274.921 Time 0.06
+Total time: 0.08 seconds Unique: 6/6 Bad splits: 0/3

test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log

@@ -18,6 +18,6 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -968.466 NNIs 0 max delta 0.00 Time 0.03
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -968.442 NNIs 0 max delta 0.00 Time 0.03 (final)
+ML-NNI round 3: LogLk = -968.442 NNIs 0 max delta 0.00 Time 0.04 (final)
 Optimize all lengths: LogLk = -968.442 Time 0.04
-Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5
+Total time: 0.05 seconds Unique: 8/8 Bad splits: 0/5