partis-bcr 1.0.13__cp312-cp312-manylinux1_x86_64.whl → 1.0.13.post1.dev2__cp312-cp312-manylinux1_x86_64.whl

{partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.13
+Version: 1.0.13.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-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.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.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.dev2.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
+partis_bcr-1.0.13.post1.dev2.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
+partis_bcr-1.0.13.post1.dev2.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
+partis_bcr-1.0.13.post1.dev2.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
+partis_bcr-1.0.13.post1.dev2.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
+partis_bcr-1.0.13.post1.dev2.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
+partis_bcr-1.0.13.post1.dev2.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
+partis_bcr-1.0.13.post1.dev2.data/scripts/partis-test.py,sha256=ORpG0LjV1PzejY36rO8-Oi3katwOzygDFtcXSst9S_0,64311
+partis_bcr-1.0.13.post1.dev2.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
+partis_bcr-1.0.13.post1.dev2.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=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
@@ -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=Aj6p5XgnRCJSUfzbKLjSg7tx4Tjb8Ic_L0AdHzeZlvI,255
+test/new-results/run-times.csv,sha256=rY1ItlyhBYS-PVoiSNnc7j3I28oXkotRQZo997sy_Ls,255
 test/new-results/seed-partition-new-simu.yaml,sha256=_OKhRdWnk6Ez1ntXXj3PFnbXZcepKYvtsi5nURN84v0,10671
-test/new-results/test.log,sha256=EaYab66pV82gt5OMzihCvTxlzzRzYdQDQ2RGvTTLbNs,20450
+test/new-results/test.log,sha256=skAZIxqM97G7uIOKWcgSicBdnnAFr-PGzuTnCamgoo8,20450
 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=YFV0LHSqsb0vjeByOOmhgKgNpG5E7LnzN3OdUHZufT4,1606
+test/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=hch57koaaMvPty0BGwkynhbrnuT5cohKZYQogYzIQTI,1606
 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
 test/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=kHcgTG5rI8nO288vbJM7fDs_gImQVbdqnlbLiNb38wg,1603
 test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out,sha256=1Fxnshag3NMB9hMWm8645aq0vWxNO7hlOqY7H4CWf3g,227
 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
+test/new-results/partition-new-simu/fasttree/iclust-2/log,sha256=T1QYu8X9eIaY6RdciTyM3WexOS-Jr_j9dGdCfNEvwdg,1561
 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=pPLqsoWr7MChKJCeXfFDEo6JS4IG21TgmLzoMi5-vdQ,12593
-test/paired/new-results/run-times.csv,sha256=w6L9n3ZgK8wjlgOvPprz8eAWSxXN5oE5Q0OeT5M9vUM,208
-test/paired/new-results/test.log,sha256=hw4oCbB4HN19x9yz3DKNvKzNA6yoy48ZrPbepLaOXaU,84806
+test/paired/new-results/run-times.csv,sha256=zocw0NsS-ca9XB9bKyA2Qr5dJ7NZ57h45nLEKDOlhZg,208
+test/paired/new-results/test.log,sha256=vLhZaJTPHIkFTuMz_9zBc4gsRsekKrwB-LpDenUWq3c,84646
 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
@@ -1003,20 +1003,20 @@ 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
-test/paired/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=QIPmVykeZ7qROEymdRIld00BuqAza3ipI1AWZpb_e2M,1534
+test/paired/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=-zBeSfTWmCs-6IqHOi1F2YADR4zdpLLqoFSUga_hVJY,1534
 test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out,sha256=TKmB3fknPQhsEkQnHyp37K4pfWGMi76t_lP1QEE0PFM,332
 test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa,sha256=hea0QDRuHtC6QGk7rioaP-qoH6JotckBqySdtILzyV8,6038
-test/paired/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=ou_xxqXaZukRTI1w7eqlqmq0-kTNCasOjtqgC2mJ85A,1535
+test/paired/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=E4yFxa4cl6p1uxX7JqLR619guuFkVnJHxCd8b4kp8kY,1535
 test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out,sha256=8iAGmWkl8Cw1An8YerCdGi3dYbBCqM03erljLmfZch0,234
 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=25KZIP4HeKCMxU4DesdGXYNygTysU6ZT4VMYzmWlgDA,1535
+test/paired/new-results/partition-new-simu/fasttree/iclust-2/log,sha256=Ul8HYFJTP6Efp2dbz4kccx7tbQJ8EcyFDqo4HgFDdvE,1535
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml,sha256=qnyJc6r4fEij37iP8yKvwXdXa6oz1GlprIABjBvEac4,5954
 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=1cTAXjSz2J7eW7WYV9a1HOnBArqlO66a9M3HQiMTuA0,4635
 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
 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=vO7VmqU3ovUHv5eeBQjBL4_OkUPmSrkzRJA-ygBuRy0,1693
+test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log,sha256=rNM0WlJY_J4vfSqWUBU5F2pzIUEucBo0oNcYt3XyjQM,1693
 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
 test/paired/new-results/partition-new-simu-annotation-performance/plots.html,sha256=yyz8jow57HiaV1_N9RX0jn6vkR_dY0pkzr8KmBxCYlo,3143
-test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg,sha256=0NVOMQDtikv5advewRmL1EsCO0j8Q709AA_eVxjjY2w,29145
-test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg,sha256=dy41cEcR_x6tUWFS4c_1dmBxmwroph7nichoVJ-n77k,22992
-test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg,sha256=SA_Lz6jyPRhn208tcTG4LATPdPNHXEPwkGVbd636IsM,19194
+test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg,sha256=iK2kIm1i1H7DZ3gGG4PhKdteDRerQNA0VSShtFSkEUI,29145
+test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg,sha256=Zv7YjmfLTV_Lf8NTqetPWkX0s4eKaNX275HrMw5sW48,22992
+test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg,sha256=8FodMKvNyUWt9KNKwSfx4mBTKOm7fKU3wx2IdzgqTNg,19194
 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
 test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.csv,sha256=gXd78-EldIOv2K-BxoAnbGc5AZwVMvkyntT1r_p9hbs,126
-test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg,sha256=hOE8FN08u2K2K_a8-Rj4LckyjaUP5gJEPfds_S0f_yQ,7107
+test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg,sha256=fGNbyZqy_jg5xDo3ZmAxqB4IZn0NPJO6FPy2NDNtSkI,7107
 test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.csv,sha256=Cs0ubrzBHEZfguO-l9_EO8-tzijl7Ih1APSVTEafBm8,183
-test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg,sha256=4uu4bx3j09qGJWeV0UnWewuvPBJgHsSUdEfS_HrLxjg,8608
-test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg,sha256=Q13a0su--1cC4zjyPll9BaOGO224ZxfURxRuIwu-ldE,13540
+test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg,sha256=8PlliRaFB_2O6n4SXCHsHHWx6QtKxLNSQmqlfdGLih4,8608
+test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg,sha256=GijNVhMRiruVhIs2u6fMErlrIAXCKisW4rfG0IuqTLQ,13540
 test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.csv,sha256=m73KMZ-S024dBjp6ulZUucAc38ZQwsDXYG2sbJGQMos,180
-test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg,sha256=OvoH58VErcsuvAYl9eCt98ui0Vj1w3IytiWRjub8uNI,7763
+test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg,sha256=x-s1gM9OUfJbUm2HQwhx5Xheyx-FDvPPVV9_fl9XRDk,7763
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.csv,sha256=Apzy9JVSmNsEdPoVZxITXt6FZ4nVcwnrDvjMVw8yH-E,371
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg,sha256=uUjK-RzP9gHt6Q7u-VpJ43eHWxouXQi7gUucCKeSCyc,12644
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg,sha256=-9fCZmtdWBCXOaWq0E3YRFKFbFioeUnAnKWov7W58xI,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=PCqjVYNgZy2kP_ATAJmqD1Ti_tzqak3Z4koTwtgIfMk,12631
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg,sha256=KleDlAZhNi9X7UHMhNrfLvILksHMdpuz3NK3KVvg1cA,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=xn2E9Da3M_CDasRH7oPDFZ0gHfm-kXM5KwiO0pRXQpU,12648
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg,sha256=NB_iDyVl6kqU4Mc7KnzbxU2Ce0CyDt7UK6ADgNuPMEE,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=yZhPJEVXbSiei1HdWc_Esp5KTycXzLQfE8vCqd86ilk,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg,sha256=MVklA9u1O8cGFVeHxwWSYnuTnFpbzhnEf1UoNrxJL08,7249
 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=bzkgEHv6bnAIqvQhYoNh2XVshIgtqQFBNAs3Di9BDqo,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg,sha256=H8Cgi2pbIwVluygyIV2Qd5QOwEZLqeIrR2ocL77oGGs,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=rpbinYNIIn1rbD-Ig-2pKMv0gczeOxw0DVRFfQQQDpw,13482
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg,sha256=bBAsLJumJbrOjfgrQevoMEAYhOxBVBt409qNCMtuKcs,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=x9tfceaUyd2om9lkKuvayaLe30dedSbdRpWWvSK6OPQ,13931
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg,sha256=VgJ4190o6LYHsBf8zbGTGnsvoC6lkeuMdUkDyl9jpUs,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=IFbZQCahrLYoWb4Jg_57FXHWhx10leYdvrTPhkibYC4,9771
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=y_YenUnQ46dhF9_52F_ms1xFTHRhmIQVdQbf_Wm8s6Q,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=M9cgR_hR5sr8vnPUF20eoqo5NRuK9tBdTLr88tuyzpI,30344
+test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=BOUPrWVQI02W9RYBRLbtBatsANwcGRQ7gXbzVcAc74c,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=EBL5WqKbNv8FsHHE8LXEVXJXruc-RNXeeNToHJQSjcc,24093
+test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=_Yu7XlwwByfUyM9SA_ZflpNqQ_UyLaUWLzCixyB_LIw,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=b9tBMtCXSe3FIT7don5Ju-oSxqliK73vCb0tB_vNDH0,24041
+test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=CoglnumZjpiRDrhX57mWmytuAAo2__YZ_MS25dhClJ8,23969
 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=NFv8soMyjVMdo8_9JbZfVfN5YkKYYsL9biLuZNqBiyA,140730
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=hOVuat7BKRDZsTsm4HiAOllAQ0KW_uGv2b1drT_tb-A,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=jTzdJ8hBeiqwrKoe4Z9LzaqH5kA4uhZP1_LjvKu4Qhw,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=-rMaZOuFzW0FDnptbx3V7OrMC9ak7lp-ZQqmUk37NI4,44439
 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.dist-info/METADATA,sha256=pxYl-D456L0qwiG6VKINxSsnHB0JVUCTUd4_sloWXrg,5008
-partis_bcr-1.0.13.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
-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.dev2.dist-info/METADATA,sha256=bj9rV8djxN5cvPOWJF3HoeI0uFdRA5N75y7aemZqG0Q,5019
+partis_bcr-1.0.13.post1.dev2.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
+partis_bcr-1.0.13.post1.dev2.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.13.post1.dev2.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.13.post1.dev2.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

@@ -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 0.04 (final)
-Optimize all lengths: LogLk = -655.501 Time 0.04
-Total time: 0.05 seconds Unique: 8/12 Bad splits: 0/5
+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

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,5.5
-annotate-new-simu,2.2
-multi-annotate-new-simu,2.1
+cache-parameters-simu,5.2
+annotate-new-simu,2.1
+multi-annotate-new-simu,1.9
 partition-new-simu,3.3
-seed-partition-new-simu,1.8
+seed-partition-new-simu,1.7
 vsearch-partition-new-simu,2.1
-get-selection-metrics-new-simu,1.6
-cache-parameters-data,6.5
-simulate,7.8
+get-selection-metrics-new-simu,1.5
+cache-parameters-data,6.4
+simulate,7.7

test/new-results/test.log

@@ -30,8 +30,8 @@ hmm
          infra time: 1.3
       hmm step time: 1.9
   writing hmms     removed 0  genes from glfo (leaving v 7  d 5  j 3)
-(0.6 sec)
-      total time: 4.0
+(0.5 sec)
+      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
@@ -49,7 +49,7 @@ 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: 0.7
+      hmm step time: 0.6
       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)
@@ -212,31 +212,31 @@ hmm
       hmm step time: 2.3
   writing hmms     removed 6  genes from glfo (leaving v 15  d 19  j 7)
 (0.7 sec)
-      total time: 5.1
+      total time: 5.0
 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 0.2s (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 0.1s (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 0.3s (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
@@ -255,13 +255,13 @@ 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 12 seqs in 0.2s (0.1s of which was running bppseqgen)
-      total time: 0.3
+      total time: 0.4
 
       --> proc 7
     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: 0.3
+      total time: 0.2
 
       --> proc 8
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
@@ -273,7 +273,7 @@ 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 4 seqs in 0.1s (0.1s of which was running bppseqgen)
-      total time: 0.2
+      total time: 0.3
 
    read 10 events with 74 seqs from 10 .yaml files
-      total time: 6.4
+      total time: 6.3

test/paired/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 = -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 0.08
-Total time: 0.10 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

@@ -16,8 +16,8 @@ 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 0.06
+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 0.07 (final)
-Optimize all lengths: LogLk = -1478.012 Time 0.07
-Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5
+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

@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
 Ignored unknown character X (seen 132 times)
 Initial topology in 0.00 seconds
 Refining topology: 10 rounds ME-NNIs, 2 rounds ME-SPRs, 5 rounds ML-NNIs
-Total branch-length 0.072 after 0.00 sec
+Total branch-length 0.072 after 0.01 sec
 ML-NNI round 1: LogLk = -1300.914 NNIs 1 max delta 0.86 Time 0.01
 GTR Frequencies: 0.2567 0.2538 0.2729 0.2166
 GTR rates(ac ag at cg ct gt) 0.8119 1.2276 0.7151 1.1364 0.4746 1.0000

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 0.04 (final)
+ML-NNI round 3: LogLk = -968.442 NNIs 0 max delta 0.00 Time 0.03 (final)
 Optimize all lengths: LogLk = -968.442 Time 0.04
-Total time: 0.05 seconds Unique: 8/8 Bad splits: 0/5
+Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5