partis-bcr 1.0.5__py3-none-any.whl → 1.0.6__py3-none-any.whl

bin/partis-test.py

@@ -33,7 +33,10 @@ class Tester(object):
     # ----------------------------------------------------------------------------------------
     def dirs(self, tstr, force_paired=False):
         assert tstr in ['ref', 'new']
-        return 'test%s/%s-results%s' % ('/paired' if (args.paired or force_paired) else '', tstr, '-slow' if args.slow else '')
+        bdir = 'test%s' % ('/paired' if (args.paired or force_paired) else '')
+        if not os.path.exists(bdir):
+            bdir = '%s/%s' % (utils.get_partis_dir(), bdir)
+        return '%s/%s-results%s' % (bdir, tstr, '-slow' if args.slow else '')
     # ----------------------------------------------------------------------------------------
     def nqr(self, act):
         if act == 'quick':  # bears no relation to the others, so makes sense to handle it differently

{partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/partis-test.py

@@ -33,7 +33,10 @@ class Tester(object):
     # ----------------------------------------------------------------------------------------
     def dirs(self, tstr, force_paired=False):
         assert tstr in ['ref', 'new']
-        return 'test%s/%s-results%s' % ('/paired' if (args.paired or force_paired) else '', tstr, '-slow' if args.slow else '')
+        bdir = 'test%s' % ('/paired' if (args.paired or force_paired) else '')
+        if not os.path.exists(bdir):
+            bdir = '%s/%s' % (utils.get_partis_dir(), bdir)
+        return '%s/%s-results%s' % (bdir, tstr, '-slow' if args.slow else '')
     # ----------------------------------------------------------------------------------------
     def nqr(self, act):
         if act == 'quick':  # bears no relation to the others, so makes sense to handle it differently

{partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.5
+Version: 1.0.6
 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-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/RECORD

@@ -23,7 +23,7 @@ bin/mds-run.py,sha256=rShy5b3oqvFZqhNdVxrtyZ4nw7whK-SKPAYl2thXooU,2003
 bin/parse-output.py,sha256=_vlx4ptHEoKiztm2RrCMqQZYlFriFmv4Sv17E6M6J9o,19533
 bin/partis,sha256=fm-5jD5mjvz3GsCeT5Q_gqeUCTCWalKgV5VJ012Xrdk,225118
 bin/partis-pip,sha256=STJkb_lm94kKxthpmIsMgFIhBWsoOJAtRJZbiFewaAU,5562
-bin/partis-test.py,sha256=NpjUMKTE2BFf2JF-WrXSOeIgIY1_WYUzv83hoawdpOA,63623
+bin/partis-test.py,sha256=CS0H2eckShv9TIPh-p_6jeaBuDd3zlRTDjaHmXU3Ln4,63749
 bin/partis.py,sha256=fm-5jD5mjvz3GsCeT5Q_gqeUCTCWalKgV5VJ012Xrdk,225118
 bin/plot-gl-set-trees.py,sha256=bgWPBmzzlD_YgWl9nQetGdzmgosXDKyVyfvaHs0VvVc,25695
 bin/plot-hmms.py,sha256=rKhPyWxexMKBt8kmwuM5ebFfFONtREoDlRqs4J52rT8,6560
@@ -297,18 +297,18 @@ data/substitution-profiles/GSSPs_for_VH_genes_with_at_least_300_lineages.txt,sha
 data/substitution-profiles/GSSPs_for_VK_genes_with_at_least_300_lineages.txt,sha256=dyMU1R_Izk_ciOVTNWmGL5SQBIKDCCKpxXM6eTGO4Fg,184138
 data/substitution-profiles/GSSPs_for_VL_genes_with_at_least_300_lineages.txt,sha256=CMFb1gk8MbfaMb6y0_qLLiKErrx866C2EafKRSPesB4,184979
 data/substitution-profiles/notes.txt,sha256=-DK9E31YovqOWaXR1Q-LL5KFhjVJcSLwXbriajUq1TA,389
-packages/ham/bcrham,sha256=4NstZkQgqdF1l_tNemIwuzVyN2zOFsw248qPoPldYWg,1194368
+packages/ham/bcrham,sha256=EfXBRtZfvPosw3I56boG6FGingnLzP-PJ5tKj1H7cxM,1194352
 packages/ig-sw/src/ig_align/ig-sw,sha256=SNFYfMlvX9s9T64t9fYIB5ugD6cZ016SZVbRhrz5Pro,293464
-partis_bcr-1.0.5.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
-partis_bcr-1.0.5.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
-partis_bcr-1.0.5.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
-partis_bcr-1.0.5.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
-partis_bcr-1.0.5.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
-partis_bcr-1.0.5.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
-partis_bcr-1.0.5.data/scripts/parse-output.py,sha256=8nrg0ip3XDhme02NCiI45BrSqCNvbRIbKYErD8STk8U,19519
-partis_bcr-1.0.5.data/scripts/partis-test.py,sha256=aI-2mLH5WXYVWoS4zateeSgDynDUC_DK9QF-UAEpWms,63609
-partis_bcr-1.0.5.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
-partis_bcr-1.0.5.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+partis_bcr-1.0.6.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
+partis_bcr-1.0.6.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
+partis_bcr-1.0.6.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
+partis_bcr-1.0.6.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
+partis_bcr-1.0.6.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
+partis_bcr-1.0.6.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
+partis_bcr-1.0.6.data/scripts/parse-output.py,sha256=8nrg0ip3XDhme02NCiI45BrSqCNvbRIbKYErD8STk8U,19519
+partis_bcr-1.0.6.data/scripts/partis-test.py,sha256=bQq_sT9v2DVQBgUGqQzdvy-q1jUrqAxV6Sl-tzENwus,63735
+partis_bcr-1.0.6.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
+partis_bcr-1.0.6.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
@@ -367,14 +367,14 @@ test/mobille-igblast-run.py,sha256=YkKISY_lQ8BbV-6lu8uoLXAtyjNayxU1x7RQ6O77phI,1
 test/phylo-naive-run.py,sha256=pTyXPv0CBddu0CVPetORRazoYyKzYa427Cwtpcuq7DE,5282
 test/run-gl-inference.sh,sha256=XK3cs5xQad5LAoVaVp2-3IMJssml8ZBNYPwLRrlW2vg,1408
 test/scoper-run.py,sha256=GzLeaGrh3IPzD9B4KC6GiS0wak8ctL7td2WJmsbb7K8,8672
-test/test.py,sha256=NpjUMKTE2BFf2JF-WrXSOeIgIY1_WYUzv83hoawdpOA,63623
+test/test.py,sha256=CS0H2eckShv9TIPh-p_6jeaBuDd3zlRTDjaHmXU3Ln4,63749
 test/new-results/annotate-new-simu.yaml,sha256=vaxN1is6V9RKzjPJI0fhSiutubXJvGXDGqPPvQjXvFw,65701
 test/new-results/cache-new-partition.csv,sha256=yfWigt-DjCePomgVZ4-1e4jcQQZuMW0R_fSVK1jqExI,20628
 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/seed-partition-new-simu.yaml,sha256=_OKhRdWnk6Ez1ntXXj3PFnbXZcepKYvtsi5nURN84v0,10671
-test/new-results/test.log,sha256=Uykk3hJ6h3JiYe9Pg5RkLGuy7Yud9wnTc25X1bSVuyw,23588
+test/new-results/test.log,sha256=g4MXQi0ZLP9FwPb_cayPQIKfq6lZQASJGPxkWk9co0k,1686
 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
@@ -799,127 +799,87 @@ test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-39_star_09.csv,sha256=
 test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-4_star_09.csv,sha256=bt6DzbGRLY9ZIZbBnuAMIcAIpKgbK_ry0P5YflZ2bmU,7823
 test/new-results/test/parameters/data/sw/mute-freqs/IGHV4-61_star_01.csv,sha256=MfxYYPSnbHtkx-7XDkXRtiC_vVWVvB0IKwUGus4wKNs,39760
 test/new-results/test/parameters/data/sw/mute-freqs/IGHV5-51_star_01.csv,sha256=WC9hZF53bWuKqT1KSgyFcW8IqkWHfqPPBSmkxLpf9wc,39848
-test/new-results/test/parameters/simu/sw-cache.yaml,sha256=dPUCPaNnXOhKKRy9Cz4abYRV7Grw9rpT-Zrwi-1PrIM,84965
-test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv,sha256=0pdxyoFEXH3_eow_rK7arPkKCuj5gluaUgPnlOzJ0v4,771
-test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv,sha256=oA9w8__2QFhKCEJUz-HvzwY9iDfSJjRHsGV9AA7vZNk,2463
-test/new-results/test/parameters/simu/hmm/all-probs.csv,sha256=HJrgmzGjmjHhMde0AQTZ30uP0ENO85ivGuawGDPFmw0,918
-test/new-results/test/parameters/simu/hmm/cluster_size.csv,sha256=RgPPs1bDG0gfsdw3swA5RZORKDE6FrdAeB0fx_p46LQ,26
-test/new-results/test/parameters/simu/hmm/d-mean-mute-freqs.csv,sha256=zgUL7HePr8fZ7DtrmqMfA5bO7MmcdMQc0_Pw6_S8lqo,873
-test/new-results/test/parameters/simu/hmm/d-mean-n-muted.csv,sha256=cHcykAwykyXRLteCC8uA6zJoJ1BiFVsVr5Bw__w87y0,269
-test/new-results/test/parameters/simu/hmm/d_gene-d_3p_del-probs.csv,sha256=8oyk1DgQK447MSpud7K-O9Rie1fFJ_tQjPH16jiSuo8,143
-test/new-results/test/parameters/simu/hmm/d_gene-d_5p_del-probs.csv,sha256=42W1P9I4nt_-cUhewABMAnqWaLjx9NwawoYnrPnXXuM,194
-test/new-results/test/parameters/simu/hmm/d_gene-probs.csv,sha256=PdTFgATwDd9px6oyyade79_4yRtvnjK0UXJB-buqaDo,90
-test/new-results/test/parameters/simu/hmm/d_gene-vd_insertion-probs.csv,sha256=i9qqNOsJrdqkM9PiH0a4RtHrhxE_N_M1qcWo4pHdFPk,217
-test/new-results/test/parameters/simu/hmm/dj_insertion_content.csv,sha256=gspVCbbXY35cvEm1HcqjofYzFKN_McQD6nYmIgFBDXg,52
-test/new-results/test/parameters/simu/hmm/fv_insertion-probs.csv,sha256=Hy8DNVuayOcpqYWC_IMR3w1Hzgjg9nO4CmTot9thkdc,37
-test/new-results/test/parameters/simu/hmm/j-mean-mute-freqs.csv,sha256=iuAAISL6SE15XJb3Dpq1IixPK6Qgo0GzvmyxWNyGUjw,840
-test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv,sha256=DJyszNfm1-piB5FES9ub2qS-Jvb4QgHZ_fkvpgTJu2U,431
-test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv,sha256=k2LpyIFpW3nJ64b_1ktCnKTub-F3FGLa7TqR7oia4ok,156
-test/new-results/test/parameters/simu/hmm/j_gene-j_3p_del-probs.csv,sha256=d4yf0G3rVZuse9YMipi-CdnmYcBbJJfZvh_cigltsXE,66
-test/new-results/test/parameters/simu/hmm/j_gene-j_5p_del-probs.csv,sha256=PWycSrYG8jrEgTdbzicNnX0SyBcXzRGHy0o1kW82f0M,124
-test/new-results/test/parameters/simu/hmm/j_gene-probs.csv,sha256=tEiCLQFJX_C0Srydy88BomF5boCpvFbt6ic_Wvxfaak,51
-test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv,sha256=IPDS23K4O_OwTi8WYSSKzLQchsxPJG8nC5cKiBPOkgk,26
-test/new-results/test/parameters/simu/hmm/seq_content.csv,sha256=am3i7V2lLccYk_uxwhx1kMMMMrypsitzKjiSpFifgU4,51
-test/new-results/test/parameters/simu/hmm/v-mean-mute-freqs.csv,sha256=G0ooefygl__ryhmyyRgDb3c2NREYOkC7fWVHbCezbn4,771
-test/new-results/test/parameters/simu/hmm/v-mean-n-muted.csv,sha256=2K3dN6XnTGHc1n6QWaVI4J_wfTON-pKMH9l3qJyjse4,1968
-test/new-results/test/parameters/simu/hmm/v_gene-probs.csv,sha256=CkPnYnmOQBArEsCuTw32tGzRxj-covPEUmuuALk9En8,118
-test/new-results/test/parameters/simu/hmm/v_gene-v_3p_del-probs.csv,sha256=WDkHin-BfQLEiJBSTqlAuFzpJLFvlgEkvvFoie4L0Q8,158
-test/new-results/test/parameters/simu/hmm/v_gene-v_5p_del-probs.csv,sha256=Vtz2eDfzLxzyuMRAJ2z_u6NL6XUqBggj5B6oUBHY9vI,141
-test/new-results/test/parameters/simu/hmm/vd_insertion_content.csv,sha256=CPTrQgZNQk0x6GWn__0m5jPdaKIATc-a0QUM3jqICOk,52
-test/new-results/test/parameters/simu/hmm/germline-sets/igh/extras.csv,sha256=36Sev7hCZRR-lcdnr9p4M--oDkqr_p2j0vGangs-7FA,246
-test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighd.fasta,sha256=E9MhkFIne6CQnCNsw5SFqyUFGuMVwqCgo1_5ZWInDkc,197
-test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighj.fasta,sha256=4UWQNkDWhOFeKG36_460WRbmJ_5BKsDi7ibAa1uhATI,196
-test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighv.fasta,sha256=xtHU6LKeyp16GSsxM749mqAy4hfAs-eimWjvss8ogy0,2165
-test/new-results/test/parameters/simu/hmm/hmms/IGHD1-20_star_01.yaml,sha256=b7HdvMzXgGFfzVhLlNpQUtLlAnPzXZNVW85bK9z_BJ4,12817
-test/new-results/test/parameters/simu/hmm/hmms/IGHD3-16_star_02.yaml,sha256=cCmSZEcCzUrJ1fMsy6XO6LFnSDOxrGNKzasMbKvxUNg,25406
-test/new-results/test/parameters/simu/hmm/hmms/IGHD3-22_star_01.yaml,sha256=60VGfvPE5nmZHH1Gzsl5A-d9oPybkByahMVt7y68jvE,21296
-test/new-results/test/parameters/simu/hmm/hmms/IGHD6-13_star_01.yaml,sha256=L43WEDCdmrXVk-5xFGo9kKReM3wHGrvEUy8mG3xVrAM,15420
-test/new-results/test/parameters/simu/hmm/hmms/IGHD6-19_star_01.yaml,sha256=_5Lwb2ax6Pa3SYXvOzxUC5e-oFBmgebTZeNBpFdgrNc,15365
-test/new-results/test/parameters/simu/hmm/hmms/IGHJ1_star_01.yaml,sha256=pYGPlWvKQIfXBhe1B6kXSoMdvY95_Tziz78rJTNYyao,24189
-test/new-results/test/parameters/simu/hmm/hmms/IGHJ4_star_02.yaml,sha256=uq0vUPwdnSpRItkF22FZmm-5cJM4BaFLpXIaB9noJXA,22386
-test/new-results/test/parameters/simu/hmm/hmms/IGHJ6_star_02.yaml,sha256=4A3DuvdlAztSO-JqajXJc1PxO1QKwabKcOEqRCDzc3Y,30701
-test/new-results/test/parameters/simu/hmm/hmms/IGHV1-18_star_01.yaml,sha256=Tv65ge9lRDVititQHEUM_KJXqoK5sDMW_ImhvkeJsBE,105925
-test/new-results/test/parameters/simu/hmm/hmms/IGHV3-23_star_01.yaml,sha256=H73YMEqxFuuzmttQ5OY7kwM7oTSNeouiRcWcof6jhK4,105405
-test/new-results/test/parameters/simu/hmm/hmms/IGHV3-66_star_02.yaml,sha256=6B6eapvjA0dm14PtqQ0wSkJIsI88xgwQdb-6iCzMYsk,99833
-test/new-results/test/parameters/simu/hmm/hmms/IGHV3-7_star_05.yaml,sha256=ieJ2eDhnn5Ub3_SnSFtmZspez9ijIgdrT6RVzwCAEXY,103495
-test/new-results/test/parameters/simu/hmm/hmms/IGHV4-4_star_09.yaml,sha256=2hFjzPwG9mbKUGGACeQIVL1twr0pFMMSd5xeGlmxD5Y,103232
-test/new-results/test/parameters/simu/hmm/hmms/IGHV4-61_star_01.yaml,sha256=F2jI_LP63_rIeejwmarK1Ja_21c2uZMcZ5jfRE9XNxY,101718
-test/new-results/test/parameters/simu/hmm/hmms/IGHV5-51_star_01.yaml,sha256=KIB7bGtCQ2PmB19ITAsVSGUsIxK-IOzazyQEGW-QR34,104913
-test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD1-20_star_01.csv,sha256=Vw0UbtEmrlYjjgBKCMERteu-WtDIQkO2EihZfdqkKlU,1179
-test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-16_star_02.csv,sha256=aFOFT0TCkp7NJgB5FWblIRqgrpLVwTL4zA8wRZ3fE4M,3935
-test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-22_star_01.csv,sha256=qSsicAv6b3ZwyJqXfbW74akt7g8JPk8_ktlUUSptoKs,4263
-test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-13_star_01.csv,sha256=l6xjzv1XB-CZ-2dMGejJ-rhTJ7gZaHhDP7lGZIsj7zY,3123
-test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-19_star_01.csv,sha256=TODqY-bHf6qXTM8qGMehBrGTtNBxWSCRkCncFyzUdck,2879
-test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ1_star_01.csv,sha256=IWDUvuCql3OWPB1CF5giAxp2MS3eDg3DiSqiZyq4HLA,6725
-test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ4_star_02.csv,sha256=AF7fTfqxHXNp66jDQZimPiSRknilJoQ8fO6ANR7qIbs,6148
-test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ6_star_02.csv,sha256=ZbxF9igVHkQej0NubNvD7nUFUTuyf49RoQRFML8mUEk,6504
-test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV1-18_star_01.csv,sha256=qWQvD-ltkpm5pNBo6oy9HCx45zn6MPuwV6F0EhKn_CQ,39176
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+test/new-results/test/parameters/simu/sw/v_gene-probs.csv,sha256=CL8bxbbHvPYuiNWvo94hWVB1mL-zITcN4RFDdExTzM0,43
+test/new-results/test/parameters/simu/sw/v_gene-v_3p_del-probs.csv,sha256=bSIfeNVOeyAKF7xxk1Lqjy31Vc0EjdReHCSzTfsO9Vw,56
+test/new-results/test/parameters/simu/sw/v_gene-v_5p_del-probs.csv,sha256=7QD0gz3Bwe7ohu9_JnKrN-lVPs2I-0MYurT6j6N-_jA,56
+test/new-results/test/parameters/simu/sw/vd_insertion_content.csv,sha256=E7qQF2I3lekkecF4aBdjT-qvvEQUiyzL-zyUPkiE2LY,50
+test/new-results/test/parameters/simu/sw/germline-sets/igh/extras.csv,sha256=WwUPAMAsd0yNibSi8vbLH0I73Tfu_tID5YuBwbdbvS4,131
+test/new-results/test/parameters/simu/sw/germline-sets/igh/ighd.fasta,sha256=ULbTkY2a57wHXpurzHZSv_E1ccVe7ykdEEgx43TD7Ro,35
+test/new-results/test/parameters/simu/sw/germline-sets/igh/ighj.fasta,sha256=nHdLzueB7Lw3B-lllse_efY9PALbL7gC2PUB4WZDwjo,133
+test/new-results/test/parameters/simu/sw/germline-sets/igh/ighv.fasta,sha256=35oLbT1k1f1DsOlh6SwgRim2YEI9GkibN88U5VtMRT8,616
+test/new-results/test/parameters/simu/sw/hmms/IGHD6-13_star_01.yaml,sha256=KYdd8QJLAmjAUFX-0WcTJTt7Z1PkHkOIuZqgPP-xGG4,15335
+test/new-results/test/parameters/simu/sw/hmms/IGHJ4_star_02.yaml,sha256=WuTEr9SU1UUrhI8quGOGT8VNANAUuB2tUlSSpigu2wk,22240
+test/new-results/test/parameters/simu/sw/hmms/IGHJ6_star_02.yaml,sha256=1NuiVXMCxs-pleS15boCvFKJCanAcohUvU_uelKYctw,30673
+test/new-results/test/parameters/simu/sw/hmms/IGHV3-66_star_02.yaml,sha256=0TA9QaIguwO8lY6ozwlBfuAJk0TFhKW5RypFt_MdpEM,104552
+test/new-results/test/parameters/simu/sw/hmms/IGHV3-7_star_05.yaml,sha256=ezh7_Ihn0PqC7msUVbcscCUOA-5rEEBMDgjpbEh3-V8,103479
+test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-13_star_01.csv,sha256=02vLfrKrqK7hf-VCdOScRm-jEBatdwgZ_aktsMytorY,2571
+test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ4_star_02.csv,sha256=dm9mGEdVG3Owp-MvEvBwbaWjhUH3qzHWSDKIpc6eUJs,5603
 test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ6_star_02.csv,sha256=-nvF_Re3o29DhELGSHCanf8UF4894aGmLvaDahgjIHo,6238
-test/new-results/test/parameters/simu/sw/mute-freqs/IGHV1-18_star_01.csv,sha256=qWQvD-ltkpm5pNBo6oy9HCx45zn6MPuwV6F0EhKn_CQ,39176
-test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-23_star_01.csv,sha256=iggcygo5zN-Wevze_vahlPZKGt7Kn2RTJ6NIMMIGq2Q,39100
-test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv,sha256=NuxSOkAlYSTLH1pYiglewkxG17C6AudeiodkogUY03o,41148
+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/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-4_star_09.csv,sha256=_2s4lvITWRfamkX32TTOzhCd_tCF7qOnY1LJ5y1jAx0,38320
-test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-61_star_01.csv,sha256=kONUU7EHhpBiHqSGDoWdTA5zBjaMYZDo385OHxsD5_w,40111
-test/new-results/test/parameters/simu/sw/mute-freqs/IGHV5-51_star_01.csv,sha256=0BOZU7pYns4oh593bGeq2V-qPaLAdH33RodQUnwDmlo,38980
 test/new-results/test/parameters/simu/true/all-mean-mute-freqs.csv,sha256=0pdxyoFEXH3_eow_rK7arPkKCuj5gluaUgPnlOzJ0v4,771
 test/new-results/test/parameters/simu/true/all-mean-n-muted.csv,sha256=q4lxyZKrQ9rXEttFW98beQBkstUDvzZhNlSwTihKwiU,2420
 test/new-results/test/parameters/simu/true/all-probs.csv,sha256=hY2LPP1S13b1EqphO0z4SSGDyERj6JCdMm3hVcKwTGM,679
@@ -7350,8 +7310,8 @@ 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-1.0.5.dist-info/METADATA,sha256=1ofeVrHOvJykH5Zf_dMy6smcfgZeDktqEmE8QQVCRfo,5024
-partis_bcr-1.0.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-partis_bcr-1.0.5.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.5.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.5.dist-info/RECORD,,
+partis_bcr-1.0.6.dist-info/METADATA,sha256=kG5P0EfVVMZYGh7F6uYhI1uPiSlpUxukWRiJ6XRD1vA,5024
+partis_bcr-1.0.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+partis_bcr-1.0.6.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.6.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.6.dist-info/RECORD,,

test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv

@@ -1,8 +1,8 @@
 bin_low_edge,contents,binlabel,error
 -0.01,0.0,,0.0
-0.0,0.3888888888888889,,0.10393492741038726
-0.01,0.4722222222222222,,0.1145307118227128
-0.02,0.1388888888888889,,0.06211299937499416
+0.0,0.0,,0.0
+0.01,0.6,,0.2449489742783178
+0.02,0.4,,0.2
 0.03,0.0,,0.0
 0.04,0.0,,0.0
 0.05,0.0,,0.0

test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv

@@ -1,16 +1,16 @@
 bin_low_edge,contents,binlabel,error
 -1.5,0.0,,0.0
--0.5,9.0,,3.0
-0.5,3.0,,1.7320508075688772
-1.5,1.0,,1.0
-2.5,1.0,,1.0
-3.5,7.0,,2.6457513110645907
-4.5,3.0,,1.7320508075688772
-5.5,5.0,,2.23606797749979
-6.5,4.0,,2.0
-7.5,2.0,,1.4142135623730951
-8.5,0.0,,0.0
-9.5,1.0,,1.0
+-0.5,0.0,,0.0
+0.5,0.0,,0.0
+1.5,0.0,,0.0
+2.5,0.0,,0.0
+3.5,2.0,,1.4142135623730951
+4.5,2.0,,1.4142135623730951
+5.5,1.0,,1.0
+6.5,3.0,,1.7320508075688772
+7.5,1.0,,1.0
+8.5,1.0,,1.0
+9.5,0.0,,0.0
 10.5,0.0,,0.0
 11.5,0.0,,0.0
 12.5,0.0,,0.0

test/new-results/test/parameters/simu/hmm/all-probs.csv

@@ -1,14 +1,4 @@
 v_gene,d_gene,j_gene,v_5p_del,v_3p_del,d_5p_del,d_3p_del,j_5p_del,j_3p_del,fv_insertion,vd_insertion,dj_insertion,jf_insertion,cdr3_length,count
-IGHV3-7*05,IGHD6-13*01,IGHJ6*02,0,0,7,0,17,0,3,4,19,0,63,1
-IGHV3-66*02,IGHD6-13*01,IGHJ4*02,0,2,3,6,8,0,6,2,1,0,33,10
-IGHV3-23*01,IGHD3-16*02,IGHJ4*02,0,0,8,0,4,0,3,0,1,0,54,2
-IGHV3-66*02,IGHD1-20*01,IGHJ4*02,0,2,3,6,8,0,6,6,7,0,39,2
-IGHV3-7*05,IGHD6-13*01,IGHJ6*02,0,0,7,0,15,0,3,4,17,0,63,1
-IGHV3-7*05,IGHD6-13*01,IGHJ6*02,0,0,9,0,17,0,3,6,19,0,63,1
-IGHV4-4*09,IGHD6-13*01,IGHJ4*02,0,3,0,6,8,0,6,10,6,0,48,1
-IGHV4-61*01,IGHD3-22*01,IGHJ1*01,0,0,0,0,3,0,0,0,0,0,60,7
-IGHV1-18*01,IGHD6-13*01,IGHJ4*02,0,0,2,5,5,0,3,9,5,0,51,7
-IGHV5-51*01,IGHD6-19*01,IGHJ4*02,0,1,0,0,5,0,3,2,3,0,48,1
-IGHV4-61*01,IGHD3-22*01,IGHJ1*01,0,0,0,0,6,0,0,0,7,0,64,1
-IGHV3-66*02,IGHD6-13*01,IGHJ4*02,0,0,2,6,8,0,6,17,7,0,57,1
-IGHV3-66*02,IGHD6-13*01,IGHJ4*02,0,2,4,6,8,0,6,3,1,0,33,1
+IGHV3-7*05,IGHD6-13*01,IGHJ6*02,0,0,7,0,17,0,0,4,19,0,63,3
+IGHV3-66*02,IGHD6-13*01,IGHJ4*02,0,2,3,6,8,0,3,2,1,0,33,6
+IGHV3-66*02,IGHD6-13*01,IGHJ4*02,0,2,4,6,8,0,3,3,1,0,33,1

test/new-results/test/parameters/simu/hmm/cluster_size.csv

@@ -1,2 +1,2 @@
 cluster_size,count
-1,36
+1,10

test/new-results/test/parameters/simu/hmm/d-mean-mute-freqs.csv

@@ -1,19 +1,19 @@
 bin_low_edge,contents,binlabel,error
 -0.01,0.0,,0.0
-0.0,0.6388888888888888,,0.1332175423142422
+0.0,0.6,,0.2449489742783178
 0.01,0.0,,0.0
 0.02,0.0,,0.0
-0.03,0.16666666666666666,,0.06804138174397717
+0.03,0.0,,0.0
 0.04,0.0,,0.0
 0.05,0.0,,0.0
-0.06,0.05555555555555555,,0.03928371006591931
-0.07,0.08333333333333333,,0.04811252243246881
-0.08,0.027777777777777776,,0.027777777777777776
+0.06,0.0,,0.0
+0.07,0.3,,0.17320508075688773
+0.08,0.1,,0.1
 0.09,0.0,,0.0
 0.1,0.0,,0.0
 0.11,0.0,,0.0
 0.12,0.0,,0.0
-0.13,0.027777777777777776,,0.027777777777777776
+0.13,0.0,,0.0
 0.14,0.0,,0.0
 0.15,0.0,,0.0
 0.16,0.0,,0.0

test/new-results/test/parameters/simu/hmm/d-mean-n-muted.csv

@@ -1,8 +1,8 @@
 bin_low_edge,contents,binlabel,error
 -1.5,0.0,,0.0
--0.5,23.0,,4.795831523312719
-0.5,10.0,,3.1622776601683795
-1.5,3.0,,1.7320508075688772
+-0.5,6.0,,2.449489742783178
+0.5,4.0,,2.0
+1.5,0.0,,0.0
 2.5,0.0,,0.0
 3.5,0.0,,0.0
 4.5,0.0,,0.0

test/new-results/test/parameters/simu/hmm/d_gene-d_3p_del-probs.csv

@@ -1,8 +1,3 @@
 d_3p_del,d_gene,count
 0,IGHD6-13*01,3
-6,IGHD6-13*01,13
-0,IGHD3-16*02,2
-6,IGHD1-20*01,2
-0,IGHD3-22*01,8
-5,IGHD6-13*01,7
-0,IGHD6-19*01,1
+6,IGHD6-13*01,7

test/new-results/test/parameters/simu/hmm/d_gene-d_5p_del-probs.csv

@@ -1,11 +1,4 @@
 d_5p_del,d_gene,count
-7,IGHD6-13*01,2
-3,IGHD6-13*01,10
-8,IGHD3-16*02,2
-3,IGHD1-20*01,2
-9,IGHD6-13*01,1
-0,IGHD6-13*01,1
-0,IGHD3-22*01,8
-2,IGHD6-13*01,8
-0,IGHD6-19*01,1
+7,IGHD6-13*01,3
+3,IGHD6-13*01,6
 4,IGHD6-13*01,1

test/new-results/test/parameters/simu/hmm/d_gene-probs.csv

@@ -1,6 +1,2 @@
 d_gene,count
-IGHD6-13*01,23
-IGHD3-16*02,2
-IGHD1-20*01,2
-IGHD3-22*01,8
-IGHD6-19*01,1
+IGHD6-13*01,10

test/new-results/test/parameters/simu/hmm/d_gene-vd_insertion-probs.csv

@@ -1,12 +1,4 @@
 vd_insertion,d_gene,count
-4,IGHD6-13*01,2
-2,IGHD6-13*01,10
-0,IGHD3-16*02,2
-6,IGHD1-20*01,2
-6,IGHD6-13*01,1
-10,IGHD6-13*01,1
-0,IGHD3-22*01,8
-9,IGHD6-13*01,7
-2,IGHD6-19*01,1
-17,IGHD6-13*01,1
+4,IGHD6-13*01,3
+2,IGHD6-13*01,6
 3,IGHD6-13*01,1

test/new-results/test/parameters/simu/hmm/dj_insertion_content.csv

@@ -1,5 +1,5 @@
 dj_insertion_content,count
-A,17
-C,57
-G,22
-T,44
+A,11
+C,16
+G,16
+T,21

test/new-results/test/parameters/simu/hmm/fv_insertion-probs.csv

@@ -1,4 +1,3 @@
 fv_insertion,count
-3,13
-6,15
-0,8
+0,3
+3,7

test/new-results/test/parameters/simu/hmm/germline-sets/igh/extras.csv

@@ -1,11 +1,5 @@
 gene,cyst_position,tryp_position,phen_position,aligned_seq
-IGHV1-18*01,285,,,
 IGHV3-7*05,285,,,
-IGHV5-51*01,285,,,
 IGHV3-66*02,282,,,
-IGHV3-23*01,285,,,
-IGHV4-61*01,288,,,
-IGHV4-4*09,282,,,
 IGHJ4*02,,14,,
 IGHJ6*02,,29,,
-IGHJ1*01,,18,,

test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighd.fasta

@@ -1,10 +1,2 @@
->IGHD1-20*01
-GGTATAACTGGAACGAC
->IGHD3-16*02
-GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC
->IGHD3-22*01
-GTATTACTATGATAGTAGTGGTTATTACTAC
 >IGHD6-13*01
 GGGTATAGCAGCAGCTGGTAC
->IGHD6-19*01
-GGGTATAGCAGTGGCTGGTAC

test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighj.fasta

@@ -1,5 +1,3 @@
->IGHJ1*01
-GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
 >IGHJ4*02
 ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
 >IGHJ6*02

test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighv.fasta

@@ -1,14 +1,4 @@
->IGHV1-18*01
-CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA
->IGHV3-23*01
-GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA
 >IGHV3-66*02
 GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA
 >IGHV3-7*05
 GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA
->IGHV4-4*09
-CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA
->IGHV4-61*01
-CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA
->IGHV5-51*01
-GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA