partis-bcr 1.0.13.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.13.post1.dev3__cp312-cp312-manylinux1_x86_64.whl

{partis_bcr-1.0.13.post1.dev1.dist-info → partis_bcr-1.0.13.post1.dev3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.13.post1.dev1
+Version: 1.0.13.post1.dev3
 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.post1.dev1.dist-info → partis_bcr-1.0.13.post1.dev3.dist-info}/RECORD

@@ -316,16 +316,16 @@ 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=4Zl5IqQ85_FMz39Dx-O-tgvULN-RVS5U9pCeiTveK-A,852320
 packages/ig-sw/src/ig_align/ig-sw,sha256=lYbqn7wujB6j1T7BGeeCqw5kwbPFn0213lDfUBmJb98,282048
-partis_bcr-1.0.13.post1.dev1.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
-partis_bcr-1.0.13.post1.dev1.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
-partis_bcr-1.0.13.post1.dev1.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
-partis_bcr-1.0.13.post1.dev1.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
-partis_bcr-1.0.13.post1.dev1.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
-partis_bcr-1.0.13.post1.dev1.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
-partis_bcr-1.0.13.post1.dev1.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
-partis_bcr-1.0.13.post1.dev1.data/scripts/partis-test.py,sha256=ORpG0LjV1PzejY36rO8-Oi3katwOzygDFtcXSst9S_0,64311
-partis_bcr-1.0.13.post1.dev1.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
-partis_bcr-1.0.13.post1.dev1.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+partis_bcr-1.0.13.post1.dev3.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
+partis_bcr-1.0.13.post1.dev3.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
+partis_bcr-1.0.13.post1.dev3.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
+partis_bcr-1.0.13.post1.dev3.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
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+partis_bcr-1.0.13.post1.dev3.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
+partis_bcr-1.0.13.post1.dev3.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
+partis_bcr-1.0.13.post1.dev3.data/scripts/partis-test.py,sha256=ORpG0LjV1PzejY36rO8-Oi3katwOzygDFtcXSst9S_0,64311
+partis_bcr-1.0.13.post1.dev3.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
+partis_bcr-1.0.13.post1.dev3.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
@@ -357,7 +357,7 @@ 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=kg9D3I0Zmt_noq4aKtUJ94TJk5T49B09gqpxpG_bdHI,49686
+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
@@ -391,9 +391,9 @@ test/new-results/cache-new-partition.csv,sha256=jHVEFlsBiSpjesVSFycef8WPFOc47b2B
 test/new-results/get-selection-metrics-new-simu.yaml,sha256=gePaoouvce-7rcq4_R_yM126SAFmmoqxqhDcjyVQwGs,8670
 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=0KbRMVFjFRIvrMzcbwKGsyqGAaeCOXxn9TWYbcvvPV8,255
+test/new-results/run-times.csv,sha256=eHrLHH7wwFJtQeizvmklYh24QwNwS89py2_UCFlP94g,255
 test/new-results/seed-partition-new-simu.yaml,sha256=_OKhRdWnk6Ez1ntXXj3PFnbXZcepKYvtsi5nURN84v0,10671
-test/new-results/test.log,sha256=COpTKOu_dCnUiGYDFF0ux_ICMFjtTKPEmHPD9wu5MAU,20450
+test/new-results/test.log,sha256=pQFeDl0KaCSxKZNxXE5YtIFTUmH24FW4wLzrD59kkG4,20450
 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
@@ -515,13 +515,13 @@ 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=XcHH5evr0molo9Y8cspuB3_RVy9z61LP47CPYnnJyrE,299
 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=hch57koaaMvPty0BGwkynhbrnuT5cohKZYQogYzIQTI,1606
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 test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out,sha256=5z3K5mwEqkWO2UjHzeQopmc52vsptbIy7eg0dRMoVv0,138
 test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa,sha256=PbcyyZtEcJqvPm8PLFeZDbICNpKJxJCMyfhdV3-dY_I,3061
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 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=9dd7zxhyIsb447frmI8z6ctsD_XlbA_7cel8D3ZPqiU,1561
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 test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv,sha256=ybPnGto_Ly4XhxcAaF48lH-eTqnlFi7GDvJ4f9dXP9Y,153
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 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=pPLqsoWr7MChKJCeXfFDEo6JS4IG21TgmLzoMi5-vdQ,12593
-test/paired/new-results/run-times.csv,sha256=5OG-RiYpdzpFQl-vSmJU8LSkjkd3EKRAS892KGCa7zM,208
-test/paired/new-results/test.log,sha256=MxYsxO-oO1TiJNa8cvJ-oNCXswf6a03HoIyyXOx9w6Y,84646
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 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
@@ -1003,10 +1003,10 @@ 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=PhTFRztnys3BZK9tDAeVNT08qfbpwqVTF-B5yjBIosI,332
 test/paired/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa,sha256=uHZPu9HHvPAYd4yBC8o-FOdG0jH4ACJcCMhA4dmvvlY,5918
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 test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa,sha256=hea0QDRuHtC6QGk7rioaP-qoH6JotckBqySdtILzyV8,6038
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@@ -1016,7 +1016,7 @@ test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metri
 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=GKZl2RGjnvAsoRfLZEkKbdkJIqBXXQPMO8jbaobGBOw,255
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 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out,sha256=R_clhMra-ApsWz9L57q5eee5ouu2TRfhss6AEPherxA,217
 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=zgD1BlZXS-lbKW1wD2aConItqnmcQLMp_D4OZB8DmE8,1692
@@ -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
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 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/true-pair-clean-performance-correct-family.csv,sha256=Apzy9JVSmNsEdPoVZxITXt6FZ4nVcwnrDvjMVw8yH-E,371
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+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg,sha256=mVZQkX6pm2dfMdP8B5SSGW7-a2POl0QZsLa9fKiiFI4,12644
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.csv,sha256=Apzy9JVSmNsEdPoVZxITXt6FZ4nVcwnrDvjMVw8yH-E,371
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg,sha256=BIMCAjhUHMa1wFnL9ZrHkR6OibfJhuBaJA1VLt9Rclg,12631
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg,sha256=T4EBBESDlV6l5A5U7R7xvc3OSTp84mwdoklQaAoQ1i4,12631
 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=ZsDsjJdVXcxE6GMiULfc4tiLSFBIud0HMLr7ZDYlGS0,12648
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg,sha256=dEnuhJoLnEvDklK0HQABeTInRYRdFYYdlujaXmmXIIA,12648
 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=pNw0JrgR9Uj8STc-DcyPB9ykAmn4hFEPLsBDlbLkKUk,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg,sha256=TCRhHEvuKPTZJZ5EJol19cHZoTWV-Ht7GMFxVUgFKFM,7249
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.csv,sha256=1cg0nJL4pkiPxn3jM1c_31pxKPM47KXGZuVp7v-Qz1M,296
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg,sha256=U2vfmr5cGrLknxB8MikWapKCa65c8elTkzsSg7f9Zqc,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg,sha256=uOOd1VcFV7TtYSdKOawuJqdiXRlELJLucGsEa4u_h6w,7249
 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=9fwLmdzQRRWIuntkQDhoqjyB5lmCMUe6yNyy1BD4EKs,13482
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg,sha256=7WcuM2gV9p7q55lipWduUQn1pS2nnif_s1BmwVtYYvU,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=IRBqwMlrRptny-_2JeLpw_4FsDRaZsfEDKbHFsZvtW0,13931
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg,sha256=MOYrv0kcdfNTfr_6hKiPG9Br4uzV2bQrUZJUlsuF_L4,13931
 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=gMJupykwlxIe8jicdAvSwvVEBtYhQuZTrdhfa9PQdiY,9771
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=4owWso_JNA7FjCY1avySjPoRx5T2hXXOUwZNcFZ3w4g,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
@@ -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=CI4Nq9fJf12eqW9XYtFt4XY-diLpAReuwReg0oZEfKA,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
@@ -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=Az_3hjq_q9FsTJepVoL2jxJuKUyO7Gn4Vfa8wymR3Lk,24021
+test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=WfDiFIYAhS_76GKy877jtbTNqEkDElGfH7b62Eh2o8Y,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
@@ -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=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=LQu-FpqtYUdhuEk8us8Xr8GsLi-tdlHJw2I_lL5p-ko,23969
+test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=tpUzPsErUlX1hU9g-FMXQaftQrkcILn7KIjb5US5BRg,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
@@ -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=1NjEeUEd-IODWVsa8q61T84ktR_cCglotQN28wjSFtE,140753
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=QqdF3x5ciQg-x6RHclz_PxNh1ApLhuA0ITg6ylU1mj8,140753
 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=nlIuY4NuJG1vJvJyrK2jnKEn9Gx-kawSdG9ou9I5kjs,78754
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=RufL5jBNvWYIpVk7mt9Dc06OA4NGtJbGfOtYPbemrTI,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=vVEHPLyBuM2FLfIIgWITgGyiW3gUpE1OfL6JVN9HcBk,44439
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=6loD9aPUkL6d5t56nFwFehE_spex12lUXrfoXxbNUX0,44439
 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
@@ -8439,8 +8439,8 @@ 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.post1.dev1.dist-info/METADATA,sha256=WooHVXhCj3wR0pdOCkWGx8HhtuG_bjr_OUi7RpXRN6E,5019
-partis_bcr-1.0.13.post1.dev1.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
-partis_bcr-1.0.13.post1.dev1.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.13.post1.dev1.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.13.post1.dev1.dist-info/RECORD,,
+partis_bcr-1.0.13.post1.dev3.dist-info/METADATA,sha256=v9vRRwdgz1h4x2mC8I3LFMCvcuJfUD6w1wNpeCfnWLg,5019
+partis_bcr-1.0.13.post1.dev3.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
+partis_bcr-1.0.13.post1.dev3.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.13.post1.dev3.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.13.post1.dev3.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')

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

@@ -19,4 +19,4 @@ 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 0.04 (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,5.1
+cache-parameters-simu,5.2
 annotate-new-simu,2.0
-multi-annotate-new-simu,1.9
-partition-new-simu,3.0
+multi-annotate-new-simu,1.8
+partition-new-simu,3.1
 seed-partition-new-simu,1.6
-vsearch-partition-new-simu,1.8
+vsearch-partition-new-simu,1.9
 get-selection-metrics-new-simu,1.4
-cache-parameters-data,6.1
-simulate,7.1
+cache-parameters-data,6.2
+simulate,7.3

test/new-results/test.log

@@ -28,10 +28,10 @@ hmm
     writing parameters to test/new-results/test/parameters/simu/hmm (0.6 sec)
     writing parameters to test/new-results/test/parameters/simu/true (0.6 sec)
          infra time: 1.3
-      hmm step time: 1.8
+      hmm step time: 1.9
   writing hmms     removed 0  genes from glfo (leaving v 7  d 5  j 3)
 (0.5 sec)
-      total time: 3.8
+      total time: 3.9
 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
@@ -67,7 +67,7 @@ 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:  (0.4s) (0.1s)   plotting performance 
+  subcluster annotating 11 clusters with steps:  (0.3s) (0.1s)   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
 
@@ -141,9 +141,9 @@ hmm
       vsearch time: 0.1
 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:  (0.3s) (0.1s) (0.1s) 
+  subcluster annotating 10 clusters with steps:  (0.4s) (0.1s) (0.1s) 
     subcluster annotation time 0.5
-      total time: 0.6
+      total time: 0.7
 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).
@@ -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
@@ -211,45 +211,45 @@ hmm
          infra time: 0.8
       hmm step time: 2.2
   writing hmms     removed 6  genes from glfo (leaving v 15  d 19  j 7)
-(0.6 sec)
-      total time: 4.8
+(0.7 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
       --> proc 0
     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)
+    made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
       total time: 0.3
 
       --> proc 1
     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 5 seqs in 0.2s (0.1s of which was running bppseqgen)
+    made 1 event with 5 seqs in 0.1s (0.1s of which was running bppseqgen)
       total time: 0.3
 
       --> 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 (0.0s of which was running bppseqgen)
+    made 1 event with 2 seqs in 0.2s (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 0.3s (0.1s of which was running bppseqgen)
+    made 1 event with 11 seqs in 0.2s (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)
-      total time: 0.3
+    made 1 event with 4 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.2
 
       --> 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 (0.1s of which was running bppseqgen)
-      total time: 0.5
+      total time: 0.4
 
       --> proc 6
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
@@ -266,14 +266,14 @@ simulating
       --> proc 8
     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 5 seqs in 0.2s (0.0s of which was running bppseqgen)
+    made 1 event with 5 seqs in 0.2s (0.1s of which was running bppseqgen)
       total time: 0.3
 
       --> proc 9
     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
 
    read 10 events with 74 seqs from 10 .yaml files
-      total time: 5.9
+      total time: 6.0

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 0.06
+ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07 (final)
-Optimize all lengths: LogLk = -1661.140 Time 0.07
-Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.08 (final)
+Optimize all lengths: LogLk = -1661.140 Time 0.08
+Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5

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

@@ -9,15 +9,15 @@ Ignored unknown character X (seen 176 times)
 Initial topology in 0.00 seconds
 Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
 Total branch-length 0.116 after 0.01 sec
-ML-NNI round 1: LogLk = -1516.977 NNIs 0 max delta 0.00 Time 0.02
+ML-NNI round 1: LogLk = -1516.977 NNIs 0 max delta 0.00 Time 0.01
 GTR Frequencies: 0.2498 0.2482 0.2788 0.2231
 GTR rates(ac ag at cg ct gt) 0.7186 0.4400 0.9760 0.8085 0.8107 1.0000
 Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.652 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 = -1478.013 NNIs 0 max delta 0.00 Time 0.07
+ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.06
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.08 (final)
-Optimize all lengths: LogLk = -1478.012 Time 0.09
-Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.06 (final)
+Optimize all lengths: LogLk = -1478.012 Time 0.07
+Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5

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