partis-bcr 1.0.13__cp312-cp312-macosx_10_13_universal2.whl → 1.0.13.post1.dev4__cp312-cp312-macosx_10_13_universal2.whl

{partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.13
+Version: 1.0.13.post1.dev4
 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-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/RECORD

@@ -317,16 +317,16 @@ packages/bpp/lib/libbpp-seq.so.9,sha256=bsDlb7oSeDBAvIhuVzeJIBzcewA6IOXwonDgzK2e
 packages/bpp/lib/libbpp-seq.so.9.1.3,sha256=bsDlb7oSeDBAvIhuVzeJIBzcewA6IOXwonDgzK2eXGs,1767196
 packages/ham/bcrham,sha256=3kZbsUpwEPzVy5v1X7HH3o_0HbX5vmV-w17opGl1-wk,768288
 packages/ig-sw/src/ig_align/ig-sw,sha256=Pl5ghiN_OYvM3299ErtwOYPhoWECl3fyzIHWAKPtTKE,387408
-partis_bcr-1.0.13.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
-partis_bcr-1.0.13.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
-partis_bcr-1.0.13.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
-partis_bcr-1.0.13.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
-partis_bcr-1.0.13.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
-partis_bcr-1.0.13.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
-partis_bcr-1.0.13.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
-partis_bcr-1.0.13.data/scripts/partis-test.py,sha256=ORpG0LjV1PzejY36rO8-Oi3katwOzygDFtcXSst9S_0,64311
-partis_bcr-1.0.13.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
-partis_bcr-1.0.13.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+partis_bcr-1.0.13.post1.dev4.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
+partis_bcr-1.0.13.post1.dev4.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
+partis_bcr-1.0.13.post1.dev4.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
+partis_bcr-1.0.13.post1.dev4.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
+partis_bcr-1.0.13.post1.dev4.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
+partis_bcr-1.0.13.post1.dev4.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
+partis_bcr-1.0.13.post1.dev4.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
+partis_bcr-1.0.13.post1.dev4.data/scripts/partis-test.py,sha256=ORpG0LjV1PzejY36rO8-Oi3katwOzygDFtcXSst9S_0,64311
+partis_bcr-1.0.13.post1.dev4.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
+partis_bcr-1.0.13.post1.dev4.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
 python/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 python/alleleclusterer.py,sha256=x50E_lJMlKPc-CPkdkM1qe4AvVi-mkDJ1cBDxs5L-ms,30551
 python/allelefinder.py,sha256=SgJjopk5ivLOcmTumsWq5PZ05aPZ6zQyjTd1fxeRjaM,80402
@@ -358,7 +358,7 @@ python/partitionplotter.py,sha256=CEfPtCCpMGbW7l6j3uOoAqmngQ5GrLWDcFTc4gLnI6o,87
 python/performanceplotter.py,sha256=bWGwodNhbZpgSlZVyfmxhpwhCGRKcJHpdl3sPiEbcnQ,20393
 python/plotconfig.py,sha256=D-QwV4xm57Gby9Cv49wDaGX2SPCxGC24c8VuNoARh7w,7945
 python/plotting.py,sha256=I9mWkyCWEMOvxFqDiO3J1qqh_1awJ8VK9rCYtLDy8Jw,114243
-python/processargs.py,sha256=Qc9okkbnLRv1GVBeMtZIzDkGcdHvryDsXiT0t9DwFss,49376
+python/processargs.py,sha256=6EzYIaf7GsG3AJuajwfg-FeLbZB3ql5KWZnMFgSKbRk,49714
 python/prutils.py,sha256=oqzL_F4zY-vxGLW-x7dEQA-YQU9QmS-UxB2kxPEUnac,22297
 python/recombinator.py,sha256=4tPAoenvOq0AQO6NVJjd77-0E-8GTFXdpAMkGdSM9TA,71838
 python/scanplot.py,sha256=-ZXle3lW5C2ZRECC6r0xJokscZT0-A_VV7om6We_HbY,64864
@@ -392,9 +392,9 @@ test/new-results/cache-new-partition.csv,sha256=jHVEFlsBiSpjesVSFycef8WPFOc47b2B
 test/new-results/get-selection-metrics-new-simu.yaml,sha256=Rhg9agnpuFIQfNs6LUhUrxJBM1WwwHMPkxYGAVQKjSE,8793
 test/new-results/multi-annotate-new-simu.yaml,sha256=dBpOYLfvkma-Tfy-DNAxsf7zB8niCRbuFSEbvSvsDLE,37319
 test/new-results/partition-new-simu.yaml,sha256=oQ1MSYpR_1ArYPfoLGYFBwaNDOrCcQ9IY0Rij75CJD8,37726
-test/new-results/run-times.csv,sha256=kOsP6OJQELwtvGMaNR6jHvCF0suZ3OnuX__sri5DMjU,242
+test/new-results/run-times.csv,sha256=K14Mmh9Y1KTsfYYPPrXbMFZjI5L09DhN7Js0OYPYNkQ,242
 test/new-results/seed-partition-new-simu.yaml,sha256=_OKhRdWnk6Ez1ntXXj3PFnbXZcepKYvtsi5nURN84v0,10671
-test/new-results/test.log,sha256=o5yexPdhCbQkhmB7mMqdcOxdmWcXDeIEB3rjsASnl68,16442
+test/new-results/test.log,sha256=3wom8222ZX89PO1si04FXaxfih9pz0e0jAiXJ5S2o6k,16441
 test/new-results/vsearch-partition-new-simu.yaml,sha256=8TCi7_M9ozjXkK82q2vdMD4yUgxwmjjORXPJVmrgReY,36290
 test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv,sha256=ybPnGto_Ly4XhxcAaF48lH-eTqnlFi7GDvJ4f9dXP9Y,153
 test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv,sha256=G1sT72mKm3q7QcXXDsDGdwbD-arhzQBV5k7id54LB_g,166
@@ -516,13 +516,13 @@ test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_ha
 test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv,sha256=mm4bOAHI1yTIte2PooOSreMdTOTommH4cwHIJc1B4_8,97
 test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out,sha256=QJmQx7cJPHHawecL_rBOAjFKWl0nIJCUmN5k1anEUPY,351
 test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa,sha256=qokRcGSD1p1XlPUBpYFMm8HYpMKfb4ed4d5PwKMVC6E,4377
-test/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=d-Kytq61uC4E6SbITe1JIEf-mOgu_o2WCyNsOUQp_8o,1621
+test/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=DWHn1K40e5Q0ScBRgu3M07qR-syVlWFpIfuMrD5pwUE,1621
 test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out,sha256=-TUcER8ZpLIDs4m4DmUydLXjtL70vx73ebTuB-KMZfE,150
 test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa,sha256=PbcyyZtEcJqvPm8PLFeZDbICNpKJxJCMyfhdV3-dY_I,3061
-test/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=kimfulsRMHb-bj8Z7Y6hxgKGtSu2xOAHD-aGEI-SLSs,1618
+test/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=QRZZtA7BNoQqE0qAwVi2xIGdQ7z6zdhPPvT7-SQW0b8,1618
 test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out,sha256=hMJ15y6H0hZmELwThgvWl2Vpb2FkzIxwk7667oSuscc,279
 test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa,sha256=UdE9X7VYtEqKx8zo0lP2gQh9mTnpsrT_R8p0jkS_wgs,3133
-test/new-results/partition-new-simu/fasttree/iclust-2/log,sha256=pcLuXOuvJugR9JbAqs52_gClt0GYGXBUq9jUS2ymKZc,1576
+test/new-results/partition-new-simu/fasttree/iclust-2/log,sha256=aDTtZ-g1lGusVEP4P90hPnJi3JW4g04WW-JEBC8H-2Q,1576
 test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv,sha256=ybPnGto_Ly4XhxcAaF48lH-eTqnlFi7GDvJ4f9dXP9Y,153
 test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv,sha256=9e7Kaol7R2sSaGRrdfRmRXRQmLKuIexslXo55oW3vv4,125
 test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv,sha256=1uCusAdxgbGGytCri7146q90JBg6SQ2Od8Gfkj4TCp8,194
@@ -987,8 +987,8 @@ 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
 test/new-results/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv,sha256=0BOZU7pYns4oh593bGeq2V-qPaLAdH33RodQUnwDmlo,38980
 test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv,sha256=1OOMLjMahLNNNKO_5-S9SnpiH4ep2t_SkGWMIr3yHVY,12599
-test/paired/new-results/run-times.csv,sha256=NTSWoP7Me2smFF_-Tzr9HsaSeQx4aoxGQOsznVN4Kvo,195
-test/paired/new-results/test.log,sha256=z_EDoaC41lmR2TmGcyopnrnKaBpj8qWhEdxMK1xJ8GM,72398
+test/paired/new-results/run-times.csv,sha256=oSOBKzgkqPYyJGWz800xCimFlWGm2s6_bbIhUEQ5kik,195
+test/paired/new-results/test.log,sha256=Zdexu3kUDHX1UvF1TbNZlH_fzAdRiat50YLz9uaqkZ8,72235
 test/paired/new-results/partition-new-simu/partition-igh.yaml,sha256=qelM_0rtDDwpLWl6_ItvkrXioZ9MI6VMiLPMf6tcbIs,71140
 test/paired/new-results/partition-new-simu/partition-igk.yaml,sha256=9iTcIjgyiVsoADqym9El14fwDT4nU_xu2mWy_UeVHSA,46688
 test/paired/new-results/partition-new-simu/partition-igl.yaml,sha256=XdV7rr3fQJPi3-5NvCxhHI4k5huOja8zxdI9XHWatMQ,23871
@@ -1003,26 +1003,26 @@ test/paired/new-results/partition-new-simu/true-pair-clean-performance-unpaired.
 test/paired/new-results/partition-new-simu/true-pair-clean-performance.csv,sha256=EgjeHR05wFVPUvq8acCzf2LhT4c7niHXpEIoc9XyX9Q,178
 test/paired/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out,sha256=mqkth6pswWx75TJwW1dE_H2HQiy_d1ovFNDPJ6UlJmM,384
 test/paired/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa,sha256=uHZPu9HHvPAYd4yBC8o-FOdG0jH4ACJcCMhA4dmvvlY,5918
-test/paired/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=psGp0-w3IW5DULIuUs_587m9o7qeTywdFq4X3tiDTCc,1546
+test/paired/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=qibHlOA04zulsDy_r0_-A5Bcq6-QBJQx_2E7W83yH7A,1546
 test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out,sha256=xmiiUt1hmQWLTOkbSt8J-9gsyE0sMhu0gNR1zxwUeDs,384
 test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa,sha256=hea0QDRuHtC6QGk7rioaP-qoH6JotckBqySdtILzyV8,6038
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 test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out,sha256=-7o36fTja9fprw6jh3E3wMWLrqED6yfDe8h-mSrVwGw,270
 test/paired/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa,sha256=XvNc2wDAuQR3Z7JnQF3QYnPxfYpQH3KzP__OfQymTcw,4434
-test/paired/new-results/partition-new-simu/fasttree/iclust-2/log,sha256=-7Hbn-GBgPdmo9camyC3UxBmYfxxtRNXToTzvMZ2GqA,1547
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 test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml,sha256=DeFoVNQJ3zbzSnuPsE8qoAvNSxalqTNYiWgyGZlV6hE,6135
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml,sha256=TvdmgfDmKq9FTXSZ8WvsP85OsORW3qB2hqMbGZG7_Ss,43157
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metrics.yaml,sha256=nnmC59opTanhhUFLO4Nz8BeKZvZ0QBr-oblRejb8eUo,4667
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk.yaml,sha256=9iTcIjgyiVsoADqym9El14fwDT4nU_xu2mWy_UeVHSA,46688
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/fasttree.out,sha256=fGk6KIDBUa5hk1-6aZQ7qCIhdU2eM-f4o6Y5hgx3v2Y,307
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/input-seqs.fa,sha256=7ENWr1tXZz6KiZ1lakxYmk6_uIniYL21PMjk_1KpcdA,3209
-test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log,sha256=If1lxp3Fqt8R7BfUR6W9A_F5Ki-8fUBPYCGq3ExpzC0,1708
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 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out,sha256=Qy5GcANnwMQQ3RMail9Te4CcLtZm-QcECudLEMDlv3w,261
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/input-seqs.fa,sha256=_AA1cnLEZd2n60CZ_FRSeUID4yggqfQyBXBbRa0ke5w,2723
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log,sha256=98xOMgDgYhpzWd5YWKJNKzvVw7izjLEwSc1fp_R2FJU,1707
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out,sha256=Y8lUkgKD485OevPo-Uvn4tA1qqOSyDyQqDeYxrenWIQ,178
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/input-seqs.fa,sha256=xmghMTcWRSKgyfKU2rnLHgIF5uDeVXOkQH2xOPKxo-o,2825
-test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log,sha256=jgYfhliFLEloWZFXWjUdmmJ0bSKerpaldWc731Te7yY,1708
+test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log,sha256=RViVBnMIzWLyFzNukrjZzV5VF5ceEkEw3LcaA9CxH6U,1708
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/fasttree.out,sha256=b9vEOyEhrsSx3ZrgAcKfiYd4Rc4pqYA-EUWP77grjjs,170
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/input-seqs.fa,sha256=911j8S0KDMzQI3X0sXXz9MTr2dzXHPP9bsr6gL-80aE,2849
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/log,sha256=_clFg90Xy3QkV4bbCa867IbJCpbjMl1UIBj6O4ai2VI,1685
@@ -1032,10 +1032,10 @@ test/paired/new-results/partition-new-simu/igh+igl/partition-igl-selection-metri
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl.yaml,sha256=XdV7rr3fQJPi3-5NvCxhHI4k5huOja8zxdI9XHWatMQ,23871
 test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/fasttree.out,sha256=WH82iKpzInHzfWc4r3U_qVEdWDZJlmQNzmkTTJKIkrY,353
 test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/input-seqs.fa,sha256=OeI88HIxr_EgFXgRB55XTg5PB8BgABcQWw9vnE-OGZM,3530
-test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log,sha256=799S8fitigSMGWzL2F95-R7qzpdVIrv_lyq1y1Pt4QA,1667
+test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log,sha256=M28oi9kPPRbG4PvjeYZO4prQHY4_buJPuUfrnkje2UQ,1667
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/fasttree.out,sha256=NHP0OvZj0TMxkdx4P9ZYz596LdXSPERT_nOWjYExxL8,332
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/input-seqs.fa,sha256=bCiUVJqUAENg7ZjDOY14bKORc4OH2ZWA1b7JKeRykKw,3152
-test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log,sha256=pYrCnwFxMUexym2JhZYobXtgooob7z4My-GBIUDV1N8,1663
+test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log,sha256=m-k0tnJwBWXcyT7-ndxJ3uvVq3yAzech6sRklDNi5UU,1663
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/fasttree.out,sha256=nat74FqovsJB8XnyWZRGF1qNToiKUgi5biRMFKnmzWc,129
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/input-seqs.fa,sha256=m8dp3ZNW6yAGnUBEYLhA0m3ZRzG05GhMknB0qddZVqY,2450
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/log,sha256=5OmPmWuNFNj5TehA0-ZshzzvUBD74vZ5C6ELksQdJ9c,982
@@ -1043,34 +1043,34 @@ test/paired/new-results/partition-new-simu/single-chain/partition-igh.yaml,sha25
 test/paired/new-results/partition-new-simu/single-chain/partition-igk.yaml,sha256=o-a0agImpMjjo32u7TaIrHbTW_RXJPkHXD8znweeT8Y,38067
 test/paired/new-results/partition-new-simu/single-chain/partition-igl.yaml,sha256=vEjx11N8dkIpx00_h5_qM4dis3254HeEsza7qkTre4I,18883
 test/paired/new-results/partition-new-simu-annotation-performance/plots.html,sha256=yyz8jow57HiaV1_N9RX0jn6vkR_dY0pkzr8KmBxCYlo,3143
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/func-per-drop.csv,sha256=hcFbqQj-_5cXQ7nwQk60LucTJs4Sjwctn8UhwGMrvjk,305
 test/paired/new-results/partition-new-simu-annotation-performance/plots/nonfunc-per-drop.csv,sha256=qBE54p878Cw8hi-DYn-Qq6NXA9go9d5-vDzDLrqc06k,318
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.csv,sha256=m73KMZ-S024dBjp6ulZUucAc38ZQwsDXYG2sbJGQMos,180
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 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=B6CZPSvNFkcbO1j_Ql3Oy_HuSj23JtF9Oea-CSZOsu4,13931
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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=BN3NMg0XnxXtv6znET_GNpvvYL0tF-nj6ncQKNv8wmE,9771
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 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
@@ -1263,7 +1263,7 @@ 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=0GKPkTETTVSNLX4qJh6VA1SqUPB4R_3oBcOzKixUtg8,30344
+test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=EtMSV8FaAHne2buH3_raceaDdg_PwQwzoaHosS0m_7M,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
@@ -1287,7 +1287,7 @@ 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=b8zrYCxbCl3hqOe7iuuddS5zlFbl-o4jBcme-y6EO0k,24838
+test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=SCD77_QESRk8c4MzemE1M-wI1s6cIp6Nma-fb3B2HgQ,24766
 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
@@ -1638,7 +1638,7 @@ 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=CjHAnWyDZtOL-D2jB_Q0j0om0qtvEhrtZcoOSbk0gSg,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=waMDDJtr4d6kqRlA2sVmg74X70COxEcOsl56iLpTh0w,24811
+test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=sS8oVMSh1N34iUDVDs1PYOSDwJp9gw9U7J_JqpH1x-E,24739
 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=mDDRdcCUT4gmdL5IQ1D2nGxXuTxdpEUvt83fNn1K35Q,27612
@@ -2007,7 +2007,7 @@ 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=NFv8soMyjVMdo8_9JbZfVfN5YkKYYsL9biLuZNqBiyA,140730
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=KaGZsdSXXJTvbWehXevpc2MWXIcj1y2hyv1vdfi8Otk,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
@@ -2041,7 +2041,7 @@ 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=NfoOwvE2MPY6Zbngae9OpjiN-cj3W3zkue7k4M1zI-4,78731
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=TMoErsoN2Y5VRvMPljea1wfhXCxlqMFU2xATpb8yUy4,78754
 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
@@ -2060,7 +2060,7 @@ 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=-lmMUa0J2xxRpjuUcA10Fxj_2xAdjd-6gp6krVTLw2w,44416
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=Vp-7UDqVp3y6gvXnq_Bx7VyBGHC2cE4smFmMhqGdwzo,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
@@ -8430,8 +8430,8 @@ 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-1.0.13.dist-info/METADATA,sha256=pxYl-D456L0qwiG6VKINxSsnHB0JVUCTUd4_sloWXrg,5008
-partis_bcr-1.0.13.dist-info/WHEEL,sha256=_N1vyLgwJ10g4JxFsp-IfU42zGJgf-DUqwfdbV1YvEM,115
-partis_bcr-1.0.13.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.13.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.13.dist-info/RECORD,,
+partis_bcr-1.0.13.post1.dev4.dist-info/METADATA,sha256=22rUjLv3PSTZpVHtVZKDMsTfjyDGaRUJjkmcT3SzG7k,5019
+partis_bcr-1.0.13.post1.dev4.dist-info/WHEEL,sha256=_N1vyLgwJ10g4JxFsp-IfU42zGJgf-DUqwfdbV1YvEM,115
+partis_bcr-1.0.13.post1.dev4.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.13.post1.dev4.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.13.post1.dev4.dist-info/RECORD,,

python/processargs.py

@@ -344,7 +344,7 @@ def process(args):
             args.aligned_germline_fname = '%s/%s/imgt-alignments/%s.fa' % (args.default_initial_germline_dir, args.species, args.locus)
         if not os.path.exists(args.aligned_germline_fname):
             raise Exception('--aligned-germline-fname %s doesn\'t exist, but we need it in order to write presto output' % args.aligned_germline_fname)
-    if not args.paired_loci and args.airr_output:
+    if not args.paired_loci and args.airr_output and not args.generate_trees:
         if args.outfname is None:
             if args.action != 'cache-parameters':
                 print('  note: no --outfname set')
@@ -466,6 +466,9 @@ def process(args):
             print('  note: no %s specified, so nothing will be written to disk' % ('--paired-outdir' if args.paired_loci else '--outfname'))
             args.outfname = get_dummy_outfname(args.workdir)  # hackey, but otherwise I have to rewrite the whole run_simulation() in bin/partis to handle None type outfname
 
+        if args.airr_output:
+            raise Exception('--airr-output isn\'t implemented for \'simulate\', but you can instead convert to airr tsv afterwards with for instance \'parse-output simu.yaml simu.tsv --airr-output\' or \'parse-output --paired <paired-simu-dir> <paired-simu-dir> --airr-output\'')
+
         if args.simulate_from_scratch:
             args.rearrange_from_scratch = True
             args.mutate_from_scratch = True

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

@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
 Ignored unknown character X (seen 48 times)
 Initial topology in 0.00 seconds
 Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
-Total branch-length 0.082 after 0.01 sec
+Total branch-length 0.082 after 0.00 sec
 ML-NNI round 1: LogLk = -667.315 NNIs 1 max delta 0.00 Time 0.01
 GTR Frequencies: 0.2215 0.2569 0.3074 0.2143
 GTR rates(ac ag at cg ct gt) 0.9744 0.9603 0.4580 0.6925 0.8029 1.0000
@@ -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 = -654.776 NNIs 1 max delta 0.00 Time 0.05
+ML-NNI round 2: LogLk = -654.776 NNIs 1 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -654.776 NNIs 0 max delta 0.00 Time 0.05 (final)
-Optimize all lengths: LogLk = -654.776 Time 0.06
-Total time: 0.08 seconds Unique: 8/12 Bad splits: 0/5
+ML-NNI round 3: LogLk = -654.776 NNIs 0 max delta 0.00 Time 0.03 (final)
+Optimize all lengths: LogLk = -654.776 Time 0.03
+Total time: 0.04 seconds Unique: 8/12 Bad splits: 0/5

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

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.624 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 = -518.489 NNIs 0 max delta 0.00 Time 0.01
+ML-NNI round 2: LogLk = -518.489 NNIs 0 max delta 0.00 Time 0.00
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -518.489 NNIs 0 max delta 0.00 Time 0.01 (final)
-Optimize all lengths: LogLk = -518.489 Time 0.01
+ML-NNI round 3: LogLk = -518.489 NNIs 0 max delta 0.00 Time 0.00 (final)
+Optimize all lengths: LogLk = -518.489 Time 0.00
 Total time: 0.01 seconds Unique: 3/8 Bad splits: 0/0

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

@@ -15,8 +15,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.636 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 = -662.208 NNIs 2 max delta 0.00 Time 0.05
+ML-NNI round 2: LogLk = -662.208 NNIs 2 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -662.208 NNIs 0 max delta 0.00 Time 0.06 (final)
-Optimize all lengths: LogLk = -662.208 Time 0.06
-Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -662.208 NNIs 0 max delta 0.00 Time 0.03 (final)
+Optimize all lengths: LogLk = -662.208 Time 0.03
+Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5

test/new-results/run-times.csv

@@ -1,9 +1,9 @@
 name,seconds
-cache-parameters-simu,9.9
-annotate-new-simu,3.9
-multi-annotate-new-simu,4.6
-partition-new-simu,8.1
-seed-partition-new-simu,4.4
-vsearch-partition-new-simu,4.3
-get-selection-metrics-new-simu,4.2
-cache-parameters-data,14.9
+cache-parameters-simu,8.1
+annotate-new-simu,3.0
+multi-annotate-new-simu,3.0
+partition-new-simu,5.8
+seed-partition-new-simu,4.0
+vsearch-partition-new-simu,4.5
+get-selection-metrics-new-simu,2.2
+cache-parameters-data,10.5

test/new-results/test.log

@@ -10,7 +10,7 @@ smith-waterman  (new-allele fitting)
     running 11 procs for 1 seq
       info for 36 / 36 = 1.000   (removed: 0 failed)
       kept 18 (0.500) unproductive
-    water time: 0.4  (ig-sw 0.0  processing 0.1)
+    water time: 0.3  (ig-sw 0.0  processing 0.2)
 smith-waterman  (writing parameters)
   vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.1 sec
     running 10 procs for 36 seqs
@@ -18,8 +18,8 @@ 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 (1.2 sec)
-    water time: 1.6  (ig-sw 1.3  processing 0.2)
+    writing parameters to test/new-results/test/parameters/simu/sw (0.9 sec)
+    water time: 1.3  (ig-sw 1.0  processing 0.2)
   writing hmms     removed 30 genes from glfo (leaving v 7  d 5  j 3)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
@@ -27,26 +27,26 @@ smith-waterman  (writing parameters)
 hmm
     reading output
         read 36 hmm output lines with 36 sequences in 36 events  (0 failures)
-    writing parameters to test/new-results/test/parameters/simu/hmm (1.5 sec)
-    writing parameters to test/new-results/test/parameters/simu/true (1.4 sec)
-         infra time: 3.0
-      hmm step time: 3.9
+    writing parameters to test/new-results/test/parameters/simu/hmm (0.9 sec)
+    writing parameters to test/new-results/test/parameters/simu/true (0.9 sec)
+         infra time: 2.0
+      hmm step time: 2.6
   writing hmms     removed 0  genes from glfo (leaving v 7  d 5  j 3)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.8 sec)
-      total time: 7.9
+(0.6 sec)
+      total time: 6.0
 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 --is-simu --plotdir test/new-results/annotate-new-simu-annotation-performance --only-csv-plots --random-seed 1 --n-procs 10 --outfname test/new-results/annotate-new-simu.yaml
 annotating    (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
-  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.1 sec
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.2 sec
         reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
       info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 18 (0.500) unproductive
   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
-        water time: 0.2
+        water time: 0.1
 hmm
     reading output
         read 36 hmm output lines with 36 sequences in 36 events  (0 failures)
@@ -54,8 +54,8 @@ hmm
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
          infra time: 0.1
-      hmm step time: 1.0
-      total time: 1.3
+      hmm step time: 0.8
+      total time: 1.1
 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
@@ -66,18 +66,18 @@ smith-waterman
       kept 18 (0.500) unproductive
   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
-(0.1 sec)
-        water time: 0.3
+(0.0 sec)
+        water time: 0.1
 hmm
   --simultaneous-true-clonal-seqs: grouping seqs according to true partition
   warning split apart 1 cluster that contained multiple cdr3 lengths (total clusters: 10 --> 11)
       cluster splits:   8 --> 7 1
-  subcluster annotating 11 clusters with steps:  (0.8s) (0.2s)   plotting performance 
+  subcluster annotating 11 clusters with steps:  (0.5s) (0.2s)   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
 
-    subcluster annotation time 1.1
-      total time: 1.5
+    subcluster annotation time 0.8
+      total time: 1.0
 partition-new-simu               partis partition --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 --max-ccf-fail-frac 0.10 --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --plotdir test/new-results/partition-new-simu-annotation-performance --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --outfname test/new-results/partition-new-simu.yaml
 partitioning     (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
@@ -88,25 +88,25 @@ smith-waterman
   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
-        water time: 0.2
+        water time: 0.1
 hmm
   --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
-  caching all 36 naive sequences (1.0s)
+  caching all 36 naive sequences (0.7s)
     collapsed 36 queries into 12 clusters with identical naive seqs (0.0 sec)
-  12 clusters with 10 procs (0.4s)
-   12 clusters with 7 procs (0.2s)
+  12 clusters with 10 procs (0.3s)
+   12 clusters with 7 procs (0.3s)
    12 clusters with 5 procs (0.2s)
    12 clusters with 3 procs (0.2s)
-   12 clusters with 2 procs (0.3s)
+   12 clusters with 2 procs (0.2s)
    11 clusters with 1 proc (0.6s)
-       partition loop time: 1.9
+       partition loop time: 1.8
 getting annotations for final partition
-  subcluster annotating 10 clusters with steps:  (0.6s) (0.2s) (0.2s)   plotting performance 
+  subcluster annotating 10 clusters with steps:  (0.4s) (0.2s) (0.2s)   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
 
-    subcluster annotation time 1.1
-      total time: 4.5
+    subcluster annotation time 1.0
+      total time: 3.9
 seed-partition-new-simu          partis partition --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 --max-ccf-fail-frac 0.10 --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --seed-unique-id 8024ed1a22 --random-seed 1 --n-procs 10 --outfname test/new-results/seed-partition-new-simu.yaml
 partitioning     (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
@@ -120,20 +120,20 @@ hmm
   --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
    collapsed 11 queries into 2 clusters with identical naive seqs (0.0 sec)
   reducing n procs to number of clusters: 10 --> 2
-  2 clusters with 2 procs (0.2s)
+  2 clusters with 2 procs (0.3s)
        removed 0 sequences in unseeded clusters, split 2 seeded clusters into 11 singletons, and merged these into 2 clusters with identical naive seqs (0.0 sec)
         new n_procs 1 (initial seqs/proc: 5.50   new seqs/proc: 2.00
-  2 clusters with 1 proc (0.2s)
-       partition loop time: 0.4
+  2 clusters with 1 proc (0.3s)
+       partition loop time: 0.5
 getting annotations for final partition
-  subcluster annotating 1 cluster with steps:  (0.3s) (0.2s) (0.2s) 
-    subcluster annotation time 0.6
+  subcluster annotating 1 cluster with steps:  (0.2s) (0.2s) (0.2s) 
+    subcluster annotation time 0.7
   seed cluster size in best partition: 11, excluding seed seq: 10
-      total time: 1.3
+      total time: 1.4
 vsearch-partition-new-simu       partis partition --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 --naive-vsearch --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --random-seed 1 --n-procs 10 --outfname test/new-results/vsearch-partition-new-simu.yaml
 partitioning     (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
-  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.2 sec
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.1 sec
         reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
       info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 18 (0.500) unproductive
@@ -143,12 +143,12 @@ hmm
         collapsed 36 sequences (36 initial naive seqs/clusters) into 12 unique naive sequences over 9 cdr3 lengths (0.0 sec)
     using hfrac bound for vsearch 0.013
     running vsearch 9 times (once for each cdr3 length class): . . . . . . . . . 
-      vsearch time: 0.2
+      vsearch time: 0.3
 getting annotations for final partition
       calculating hmm annotations even though --fast/--naive-vsearch was set (you can set --use-sw-annotations to get faster (but substantially less accurate) annotations, or set --dont-calculate-annotations if you only need the partition)
-  subcluster annotating 10 clusters with steps:  (0.6s) (0.2s) (0.2s) 
-    subcluster annotation time 1.0
-      total time: 1.6
+  subcluster annotating 10 clusters with steps:  (0.5s) (0.2s) (0.2s) 
+    subcluster annotation time 0.9
+      total time: 1.5
 get-selection-metrics-new-simu   partis get-selection-metrics --dont-write-git-info --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --outfname test/new-results/partition-new-simu.yaml --selection-metric-fname test/new-results/get-selection-metrics-new-simu.yaml
   note: --parameter-dir not set, so using default: x-dummy-x
   note: By default we print/operate on *all* annotations in the output file, which in general can include annotations from non-best partititons and non-seed clusters (e.g. if --n-final-clusters was set).
@@ -160,7 +160,7 @@ getting annotations for final partition
         run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
         run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
         run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
-      made 3 fasttree trees (0.5s)
+      made 3 fasttree trees (0.3s)
     tree origins: 3 ran fasttree
     skipped 1/4 clusters smaller than 4
       setting default tau to 1 / 352 = 0.0028
@@ -172,42 +172,42 @@ 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 eyz fnv nox
     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: 0.7
+      total time: 0.4
 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
   --input-metafnames: added meta info for 4 sequences from test/input-meta.yaml: multiplicities
 caching parameters
-  vsearch: 44 / 50 v annotations (6 failed) with 54 v genes in 0.2 sec
+  vsearch: 44 / 50 v annotations (6 failed) with 54 v genes in 0.1 sec
     keeping 24 / 198 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.2 sec
+  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.0 sec
     running 10 procs for 50 seqs
     running 12 procs for 5 seqs
       info for 46 / 50 = 0.920   (removed: 4 failed)
       kept 16 (0.320) unproductive
-    water time: 0.4  (ig-sw 0.0  processing 0.2)
+    water time: 0.3  (ig-sw 0.0  processing 0.2)
 smith-waterman  (writing parameters)
-  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.2 sec
+  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.1 sec
     running 10 procs for 46 seqs
     running 11 procs for 1 seq
       info for 46 / 50 = 0.920   (removed: 4 failed)
       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 (2.1 sec)
-    water time: 2.5  (ig-sw 2.2  processing 0.1)
+    writing parameters to test/new-results/test/parameters/data/sw (1.2 sec)
+    water time: 1.6  (ig-sw 1.3  processing 0.1)
   writing hmms     removed 15 genes from glfo (leaving v 18  d 22  j 7)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(2.4 sec)
+(1.8 sec)
 hmm
     reading output
         read 46 hmm output lines with 46 sequences in 46 events  (0 failures)
-    writing parameters to test/new-results/test/parameters/data/hmm (1.7 sec)
-         infra time: 1.8
-      hmm step time: 4.2
+    writing parameters to test/new-results/test/parameters/data/hmm (1.2 sec)
+         infra time: 1.4
+      hmm step time: 2.9
   writing hmms     removed 6  genes from glfo (leaving v 15  d 19  j 7)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(1.8 sec)
-      total time: 12.0
+(1.4 sec)
+      total time: 8.5