partis-bcr 1.0.13__cp312-cp312-manylinux1_x86_64.whl → 1.0.13.post1.dev1__cp312-cp312-manylinux1_x86_64.whl

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.13
+Version: 1.0.13.post1.dev1
 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.dev1.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.dev1.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
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+partis_bcr-1.0.13.post1.dev1.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
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-python/processargs.py,sha256=Qc9okkbnLRv1GVBeMtZIzDkGcdHvryDsXiT0t9DwFss,49376
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 python/prutils.py,sha256=oqzL_F4zY-vxGLW-x7dEQA-YQU9QmS-UxB2kxPEUnac,22297
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 python/scanplot.py,sha256=-ZXle3lW5C2ZRECC6r0xJokscZT0-A_VV7om6We_HbY,64864
@@ -391,9 +391,9 @@ test/new-results/cache-new-partition.csv,sha256=jHVEFlsBiSpjesVSFycef8WPFOc47b2B
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-test/new-results/test.log,sha256=EaYab66pV82gt5OMzihCvTxlzzRzYdQDQ2RGvTTLbNs,20450
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 test/new-results/vsearch-partition-new-simu.yaml,sha256=8TCi7_M9ozjXkK82q2vdMD4yUgxwmjjORXPJVmrgReY,36290
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@@ -515,7 +515,7 @@ test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_ha
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@@ -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
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@@ -1003,10 +1003,10 @@ test/paired/new-results/partition-new-simu/true-pair-clean-performance-unpaired.
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@@ -1016,7 +1016,7 @@ test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metri
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@@ -1043,34 +1043,34 @@ test/paired/new-results/partition-new-simu/single-chain/partition-igh.yaml,sha25
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+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-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=pNw0JrgR9Uj8STc-DcyPB9ykAmn4hFEPLsBDlbLkKUk,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=U2vfmr5cGrLknxB8MikWapKCa65c8elTkzsSg7f9Zqc,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=9fwLmdzQRRWIuntkQDhoqjyB5lmCMUe6yNyy1BD4EKs,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=IRBqwMlrRptny-_2JeLpw_4FsDRaZsfEDKbHFsZvtW0,13931
 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=gMJupykwlxIe8jicdAvSwvVEBtYhQuZTrdhfa9PQdiY,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=CI4Nq9fJf12eqW9XYtFt4XY-diLpAReuwReg0oZEfKA,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=Az_3hjq_q9FsTJepVoL2jxJuKUyO7Gn4Vfa8wymR3Lk,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=LQu-FpqtYUdhuEk8us8Xr8GsLi-tdlHJw2I_lL5p-ko,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=1NjEeUEd-IODWVsa8q61T84ktR_cCglotQN28wjSFtE,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=nlIuY4NuJG1vJvJyrK2jnKEn9Gx-kawSdG9ou9I5kjs,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=vVEHPLyBuM2FLfIIgWITgGyiW3gUpE1OfL6JVN9HcBk,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.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,,

python/processargs.py

@@ -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/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
-partition-new-simu,3.3
-seed-partition-new-simu,1.8
-vsearch-partition-new-simu,2.1
-get-selection-metrics-new-simu,1.6
-cache-parameters-data,6.5
-simulate,7.8
+cache-parameters-simu,5.1
+annotate-new-simu,2.0
+multi-annotate-new-simu,1.9
+partition-new-simu,3.0
+seed-partition-new-simu,1.6
+vsearch-partition-new-simu,1.8
+get-selection-metrics-new-simu,1.4
+cache-parameters-data,6.1
+simulate,7.1

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: 1.9
+      hmm step time: 1.8
   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: 3.8
 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
@@ -49,8 +49,8 @@ hmm
   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
-      hmm step time: 0.7
-      total time: 0.8
+      hmm step time: 0.6
+      total time: 0.7
 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
@@ -101,7 +101,7 @@ getting annotations for final partition
 (0.0 sec)
 
     subcluster annotation time 0.5
-      total time: 1.9
+      total time: 1.8
 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
@@ -143,7 +143,7 @@ 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 annotation time 0.5
-      total time: 0.7
+      total time: 0.6
 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).
@@ -178,7 +178,7 @@ getting annotations for final partition
       warning get_aa_tree() (AA inf tree, iclust 2): skipped 11/13 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: apr dhq fnv nox uvx
     skipped 1/4 clusters that had no uids in common with tree
   writing selection metrics to test/new-results/get-selection-metrics-new-simu.yaml
-      total time: 0.2
+      total time: 0.1
 cache-parameters-data            partis cache-parameters --dont-write-git-info --infname test/mishmash.fa --parameter-dir test/new-results/test/parameters/data --sw-cachefname test/new-results/test/parameters/data/sw-cache.yaml --n-max-queries 50 --input-metafnames test/input-meta.yaml --random-seed 1 --n-procs 10
     stopped after reading 50 sequences from test/mishmash.fa
   --n-max-queries: stopped after reading 50 queries from input file
@@ -209,16 +209,16 @@ hmm
         read 46 hmm output lines with 46 sequences in 46 events  (0 failures)
     writing parameters to test/new-results/test/parameters/data/hmm (0.7 sec)
          infra time: 0.8
-      hmm step time: 2.3
+      hmm step time: 2.2
   writing hmms     removed 6  genes from glfo (leaving v 15  d 19  j 7)
-(0.7 sec)
-      total time: 5.1
+(0.6 sec)
+      total time: 4.8
 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 (0.1s of which was running bppseqgen)
       total time: 0.3
 
       --> proc 1
@@ -249,7 +249,7 @@ 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 22 seqs in 0.3s (0.1s of which was running bppseqgen)
-      total time: 0.4
+      total time: 0.5
 
       --> proc 6
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
@@ -261,7 +261,7 @@ simulating
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 3 seqs in 0.1s (0.1s of which was running bppseqgen)
-      total time: 0.3
+      total time: 0.2
 
       --> proc 8
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
@@ -272,8 +272,8 @@ simulating
       --> 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 0.1s (0.1s of which was running bppseqgen)
-      total time: 0.2
+    made 1 event with 4 seqs in 0.2s (0.1s of which was running bppseqgen)
+      total time: 0.3
 
    read 10 events with 74 seqs from 10 .yaml files
-      total time: 6.4
+      total time: 5.9

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/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