partis-bcr 1.0.10__cp312-cp312-manylinux1_x86_64.whl → 1.0.11__cp312-cp312-manylinux1_x86_64.whl

bin/parse-output.py

@@ -130,7 +130,7 @@ if args.paired:
 else:
     assert utils.getsuffix(args.outfile) in ['.csv', '.tsv', '.fa', '.fasta', '.yaml'] # or args.airr_input and utils.getsuffix(args.outfile) == '.yaml'
 
-default_glfo_dir = partis_dir + '/data/germlines/human'
+default_glfo_dir = utils.get_partis_dir() + '/data/germlines/human'
 if utils.getsuffix(args.infile) in ['.csv', '.tsv'] and args.glfo_dir is None:
     print('  note: reading csv/tsv format without germline info, so need to get germline info from a separate directory; --glfo-dir was not set, so using default %s. If it doesn\'t crash, it\'s probably ok.' % default_glfo_dir)
     args.glfo_dir = default_glfo_dir
@@ -181,7 +181,7 @@ if args.paired:
             writer.writerow({k : ofo[k] for k in okeys})
     if args.airr_output:
         for ltmp in sorted(glfos):
-            utils.write_airr_output('%s/%s.tsv'%(args.outfile, ltmp), antn_lists[ltmp], cpath=cpaths[ltmp], glfo=glfos[ltmp])
+            utils.write_airr_output('%s/%s.tsv'%(args.outfile, ltmp), antn_lists[ltmp], cpath=cpaths[ltmp], glfo=glfos[ltmp], extra_columns=args.extra_columns)
     sys.exit(0)
 
 # restrict to certain partitions/clusters

{partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/parse-output.py

@@ -130,7 +130,7 @@ if args.paired:
 else:
     assert utils.getsuffix(args.outfile) in ['.csv', '.tsv', '.fa', '.fasta', '.yaml'] # or args.airr_input and utils.getsuffix(args.outfile) == '.yaml'
 
-default_glfo_dir = partis_dir + '/data/germlines/human'
+default_glfo_dir = utils.get_partis_dir() + '/data/germlines/human'
 if utils.getsuffix(args.infile) in ['.csv', '.tsv'] and args.glfo_dir is None:
     print('  note: reading csv/tsv format without germline info, so need to get germline info from a separate directory; --glfo-dir was not set, so using default %s. If it doesn\'t crash, it\'s probably ok.' % default_glfo_dir)
     args.glfo_dir = default_glfo_dir
@@ -181,7 +181,7 @@ if args.paired:
             writer.writerow({k : ofo[k] for k in okeys})
     if args.airr_output:
         for ltmp in sorted(glfos):
-            utils.write_airr_output('%s/%s.tsv'%(args.outfile, ltmp), antn_lists[ltmp], cpath=cpaths[ltmp], glfo=glfos[ltmp])
+            utils.write_airr_output('%s/%s.tsv'%(args.outfile, ltmp), antn_lists[ltmp], cpath=cpaths[ltmp], glfo=glfos[ltmp], extra_columns=args.extra_columns)
     sys.exit(0)
 
 # restrict to certain partitions/clusters

{partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.10
+Version: 1.0.11
 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-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/RECORD

@@ -24,7 +24,7 @@ bin/iqtree3_intel,sha256=QEJMzbHXnDBGQfkQy2wXLrtnAhTlCVg1IBjj_5kGq48,11333032
 bin/lonr.r,sha256=YzAsjyQ-NZ2shOPhzkFFppsgXJEhMTztFA-C6NVyEJ4,44212
 bin/makeHtml,sha256=SMMulEmYoU4ve4jlCRNaDuw9f4FS4t8g_FGE7z5Ndb4,1190
 bin/mds-run.py,sha256=rShy5b3oqvFZqhNdVxrtyZ4nw7whK-SKPAYl2thXooU,2003
-bin/parse-output.py,sha256=_vlx4ptHEoKiztm2RrCMqQZYlFriFmv4Sv17E6M6J9o,19533
+bin/parse-output.py,sha256=MzCN5H9yisRjiLcUyfcg78Xvt3Q29qTAU1LpZ6OLMMg,19579
 bin/partis,sha256=fm-5jD5mjvz3GsCeT5Q_gqeUCTCWalKgV5VJ012Xrdk,225118
 bin/partis-test.py,sha256=CS0H2eckShv9TIPh-p_6jeaBuDd3zlRTDjaHmXU3Ln4,63749
 bin/partis.py,sha256=fm-5jD5mjvz3GsCeT5Q_gqeUCTCWalKgV5VJ012Xrdk,225118
@@ -303,16 +303,16 @@ data/substitution-profiles/GSSPs_for_VL_genes_with_at_least_300_lineages.txt,sha
 data/substitution-profiles/notes.txt,sha256=-DK9E31YovqOWaXR1Q-LL5KFhjVJcSLwXbriajUq1TA,389
 packages/ham/bcrham,sha256=1g26DafyE_6wglae2TUXc6xkpd2AUp0LDV6Kl_2S7jY,852320
 packages/ig-sw/src/ig_align/ig-sw,sha256=lYbqn7wujB6j1T7BGeeCqw5kwbPFn0213lDfUBmJb98,282048
-partis_bcr-1.0.10.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
-partis_bcr-1.0.10.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
-partis_bcr-1.0.10.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
-partis_bcr-1.0.10.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
-partis_bcr-1.0.10.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
-partis_bcr-1.0.10.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
-partis_bcr-1.0.10.data/scripts/parse-output.py,sha256=8nrg0ip3XDhme02NCiI45BrSqCNvbRIbKYErD8STk8U,19519
-partis_bcr-1.0.10.data/scripts/partis-test.py,sha256=bQq_sT9v2DVQBgUGqQzdvy-q1jUrqAxV6Sl-tzENwus,63735
-partis_bcr-1.0.10.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
-partis_bcr-1.0.10.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+partis_bcr-1.0.11.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
+partis_bcr-1.0.11.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
+partis_bcr-1.0.11.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
+partis_bcr-1.0.11.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
+partis_bcr-1.0.11.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
+partis_bcr-1.0.11.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
+partis_bcr-1.0.11.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
+partis_bcr-1.0.11.data/scripts/partis-test.py,sha256=bQq_sT9v2DVQBgUGqQzdvy-q1jUrqAxV6Sl-tzENwus,63735
+partis_bcr-1.0.11.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
+partis_bcr-1.0.11.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
@@ -368,11 +368,11 @@ test/input-meta.yaml,sha256=krw3yB1ASTZiY_enV5v8S4IT9d7iYCPrQ0Dr6loHLcI,143
 test/linearham-run.py,sha256=Ts5-U3voWsGQiYB4tHS8PYGEmWz1XC3aLapcul1xh50,23831
 test/mishmash.fa,sha256=OkrgzIXOhBO0IbLUYO1BTVAnhdDiLvd_kkQgKWgRK14,319759
 test/mobille-igblast-run.py,sha256=YkKISY_lQ8BbV-6lu8uoLXAtyjNayxU1x7RQ6O77phI,13882
-test/phylo-naive-run.py,sha256=pTyXPv0CBddu0CVPetORRazoYyKzYa427Cwtpcuq7DE,5282
+test/phylo-naive-run.py,sha256=CVOuyOTbCiFINZHrTcLNvk9j-dqnXu9n9LOWvAAVA44,5303
 test/run-gl-inference.sh,sha256=XK3cs5xQad5LAoVaVp2-3IMJssml8ZBNYPwLRrlW2vg,1408
 test/scoper-run.py,sha256=GzLeaGrh3IPzD9B4KC6GiS0wak8ctL7td2WJmsbb7K8,8672
 test/test.py,sha256=CS0H2eckShv9TIPh-p_6jeaBuDd3zlRTDjaHmXU3Ln4,63749
-test/new-results/test.log,sha256=KkEUQqNiwYqaA1m5Q3jHUeMdG4oXPjPL-5ng5BAuMwA,1610
+test/new-results/test.log,sha256=PW8lc00zbHxAfwt1SVzDSy74fxhuKTpKNqqCzqmsG-o,1610
 test/new-results/test/parameters/simu/sw-cache.yaml,sha256=xRR9tZOPBIIU2d3QmiWCUcprRlXZre8BhmMONmgAcq8,24635
 test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv,sha256=9U28KM6iUMP9_3CwhOlFl5uhO2I4nBJRpKy20z5rfMc,694
 test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv,sha256=8n9PeG1kl44R8PSBy80bm-EXIUbUR2Oae53USbydt9o,2435
@@ -455,8 +455,8 @@ test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ6_star_02.csv,sha256=-nv
 test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv,sha256=L2u0w3IWDJKOshqCT6St6SxKKPAjq6JbY0JDH9uBMls,39711
 test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-7_star_05.csv,sha256=Ve6Y1IAOpf0ls0fwDtz7KMoMxrGtH2RadkomESpABR8,39704
 test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv,sha256=pPLqsoWr7MChKJCeXfFDEo6JS4IG21TgmLzoMi5-vdQ,12593
-test/paired/new-results/run-times.csv,sha256=jGD1Tj_ki4jgDehPx6F_Rhy3mKClJFC6v_hX5FdTMeY,193
-test/paired/new-results/test.log,sha256=XyH9BxH4yPphM0jVmPALHJL0jThI9a4kmDa1VLbYCjI,70880
+test/paired/new-results/run-times.csv,sha256=GqH6yQlLoO1BRz_1mauwSOsb63OmgQrg6HaKCaSX39Q,193
+test/paired/new-results/test.log,sha256=yNHGaGsimxcKh1N9fLXOcBES5OjLVNJwykIj_qGLoHA,70880
 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
@@ -474,7 +474,7 @@ test/paired/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa,sha25
 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=Nj5WS8kZzmxjC4_NQzyycO0fgaT0ALuXopckGiyVdto,1535
+test/paired/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=pfRNkbguacbLgwiJipi6V5GFx8RaRjpvP80UTpH1M0E,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
@@ -484,7 +484,7 @@ 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
 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=qGzhw1CVW1E8forP8d1sIZEwf6lBsR0v6yywIxWoLE8,1693
 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
@@ -511,34 +511,34 @@ 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=ndWvnKys1_-WtpWZnjKgCGEO5R_oaoxPhbLIscsme6k,29145
-test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg,sha256=ddR7HUs6wmoKjfwM7HN_5pL5N2RsT-HXEENi6u7v-K4,22992
-test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg,sha256=ZcxxzQImAAgoXlCk3e0jEXcYBovMDuNqe214-tHPVio,19194
+test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg,sha256=m0Bb0CAZkcz9nT4qsDLk_YdeMVMJCvtNw_p52ZcrJ-U,29145
+test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg,sha256=KXLSRxmmB9iu1ZZitX7hDhgPtJVUyTaiYEmnru18aco,22992
+test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg,sha256=jcauR1QKJVqFqcoUamHkjfV6-_NEbVOwIj3Dx50rw0s,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=heOEI8TqJqe-xsLh3rZ17J6Hp3zoB91T9wqDYuy5W8I,7107
+test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg,sha256=y37dbl7u5q4ciY3wbVPcxEAyr7bxW0m8zufDGsMhbNk,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=FQZLivlWeYdeGmVeLZ00Oy4XiXUVfvNumouzwAXDPxw,8608
-test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg,sha256=aAqHDKteWEewXdqLbsxZphBZP6JRQk3asg2-ysErKWQ,13540
+test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg,sha256=fz6vaYv4411q2_P4FSv33CRPYllI_Gx8F_xP9WsByT0,8608
+test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg,sha256=Npa769QEKkeNZHE-T2x23nK9PrgtjnYMS_kI1hsL2K0,13540
 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=KMDN_1qqmFmoB0feZ9asfcRhtTMGB5YGobojTJ4kySs,7763
+test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg,sha256=zrzMKflazpD9tWkIeOpynnK07mDc2KkY9YtwiENAYEY,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=YRyWWLVF9PM2yqemiW-goKMO86E_VCL1-pLSIF4X55k,12644
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg,sha256=InCi3XO82nCkEBU_G7ys8fshDlJ4EGBUeApywXQw0GM,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=ZOjSxv-rPqMBMyXz7Cg9a52No4_JV8qmcsIfCXMewSs,12631
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg,sha256=F4i1kvKumKWAgOA5qIAlb4Mdt1OvIAtqUplbsq_9_Sc,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=0pd8QqAbNinnRcp0pT-Gu3upE7PAyCCI9mXhG6xxwiI,12648
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg,sha256=i5RPb27Jx3Oc4TSuCMg8e0IpL9dBq2ZnmNEN_r0nsyM,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=_jDV_JdW6Pjod7LpNU3U4onAqEO9-qbQJdbKRvy_zfE,7249
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.csv,sha256=1cg0nJL4pkiPxn3jM1c_31pxKPM47KXGZuVp7v-Qz1M,296
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg,sha256=Spl7PmU4wNQ_GmNAxgGU2Sb0NkZ_urzD6M7aP5xAvXc,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg,sha256=AZrN7Wh1v68ayV-0q9XhuGjBw4c9BJEEsOeiPxAGiNg,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=0QdzercjOe877oLyLoNma40JUkfPBxDP91CyqTbrmaI,13482
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg,sha256=DWqDOEyv_EROxFIbvys86YZXZ-tPp4ackmPjct78B0I,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=UpMZ4zh4Ax7SJgns5OOxSSNyAthMs27A5cIA8mJSboY,13931
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg,sha256=ExQ053ZC7yLqb01B39iiNRkv8-aADt8M_4xqLUaoGzs,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=J-qgaeTDgB3XQi9C0z6sg0NnM2V34FR3ROCbs8Uufqs,9771
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=sXmhZmBJogUk_VukTCLHqpmMbw2mFhHm0wGkPY80HmE,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
@@ -731,7 +731,7 @@ 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=bIXfGDsH9OuQdElXNhTqzXHHIs9LmCO0Zree5FTSkow,30344
+test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=07Yq9DINmrcaq_Ti6tSBwooHKkpq9H5Zch80lR6VpDE,30344
 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
@@ -755,7 +755,7 @@ 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=f0AAE8_rNc0nlmHHQaHwS9-jeeaM53lpOAx48WE2Et4,24093
+test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=ldZJ4Ip56-8TjQf7DtkTWnQpkAQ6bX8tJq94_el3OY0,24093
 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
@@ -1106,7 +1106,7 @@ 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=8Sdfypv5i4lnA6KfbaWgeyaoVfx9y7qhs6a0mFh7U3Q,24041
+test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=JON9k3hR1F4vdVPnBARGRWmOsEccKk_iZJ0lI-Tywj8,24041
 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
@@ -1475,7 +1475,7 @@ 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=_SOA7hU9IUBBmzLSipg6qdcJSeWS6ZwaRVpvXbPly1A,140730
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=bTAyJcv8WAqZQF7MTm0q9Lxtc54RGNAiuY4N-BjtT1k,140730
 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
@@ -1509,7 +1509,7 @@ 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=h7cTkmU5TY31ovYMML9F9yQzdKUphahMPEPvMwwJENU,78731
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=r2G9w5gYkUH7E2rClnXK9kOtorQ4eDT9YRx7f09HgGA,78731
 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
@@ -1528,7 +1528,7 @@ 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=QC1tlIbqWl-FCkGC850cdWmIARzdRScV6xJUILTzLGo,44416
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=EwiOSjt-6BiOKIFBNrEWD6KNjqhb_a71YaAmCj46lM0,44416
 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
@@ -7898,8 +7898,8 @@ 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-1.0.10.dist-info/METADATA,sha256=jw9HF4E0gZy7LIkr9L9Y9Yy37J1P_e2_ObpKbFI0Fgk,5008
-partis_bcr-1.0.10.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
-partis_bcr-1.0.10.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.10.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.10.dist-info/RECORD,,
+partis_bcr-1.0.11.dist-info/METADATA,sha256=QgDlFi1DFmJM4EpY5WgBAkevB2jPqf90FmD57HEqfeo,5008
+partis_bcr-1.0.11.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
+partis_bcr-1.0.11.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.11.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.11.dist-info/RECORD,,

test/new-results/test.log

@@ -8,7 +8,7 @@ smith-waterman  (new-allele fitting)
     running 10 procs for 10 seqs
       info for 10 / 10 = 1.000   (removed: 0 failed)
       kept 10 (1.000) unproductive
-    water time: 0.1  (ig-sw 0.0  processing 0.1)
+    water time: 0.0  (ig-sw 0.0  processing 0.0)
 smith-waterman  (writing parameters)
   vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.0 sec
     running 10 procs for 10 seqs
@@ -16,7 +16,7 @@ smith-waterman  (writing parameters)
       kept 10 (1.000) unproductive
         writing sw results to test/new-results/test/parameters/simu/sw-cache.yaml
     writing parameters to test/new-results/test/parameters/simu/sw (1.3 sec)
-    water time: 1.4  (ig-sw 1.4  processing 0.0)
+    water time: 1.3  (ig-sw 1.3  processing 0.0)
   writing hmms     removed 35 genes from glfo (leaving v 2  d 1  j 2)
 (0.1 sec)
 hmm
@@ -27,4 +27,4 @@ hmm
       hmm step time: 0.4
   writing hmms     removed 0  genes from glfo (leaving v 2  d 1  j 2)
 (0.1 sec)
-      total time: 2.2
+      total time: 2.1

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

@@ -9,7 +9,7 @@ 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)
@@ -18,6 +18,6 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.07
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.09 (final)
+ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.08 (final)
 Optimize all lengths: LogLk = -1478.012 Time 0.09
 Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/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