partis-bcr 1.0.10.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.11.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl

{partis_bcr-1.0.10.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.10.post1.dev1
+Version: 1.0.11.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-1.0.10.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev1.dist-info}/RECORD

@@ -304,16 +304,16 @@ 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=3kZbsUpwEPzVy5v1X7HH3o_0HbX5vmV-w17opGl1-wk,768288
 packages/ig-sw/src/ig_align/ig-sw,sha256=Pl5ghiN_OYvM3299ErtwOYPhoWECl3fyzIHWAKPtTKE,387408
-partis_bcr-1.0.10.post1.dev1.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
-partis_bcr-1.0.10.post1.dev1.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
-partis_bcr-1.0.10.post1.dev1.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
-partis_bcr-1.0.10.post1.dev1.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
-partis_bcr-1.0.10.post1.dev1.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
-partis_bcr-1.0.10.post1.dev1.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
-partis_bcr-1.0.10.post1.dev1.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
-partis_bcr-1.0.10.post1.dev1.data/scripts/partis-test.py,sha256=bQq_sT9v2DVQBgUGqQzdvy-q1jUrqAxV6Sl-tzENwus,63735
-partis_bcr-1.0.10.post1.dev1.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
-partis_bcr-1.0.10.post1.dev1.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+partis_bcr-1.0.11.post1.dev1.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
+partis_bcr-1.0.11.post1.dev1.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
+partis_bcr-1.0.11.post1.dev1.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
+partis_bcr-1.0.11.post1.dev1.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
+partis_bcr-1.0.11.post1.dev1.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
+partis_bcr-1.0.11.post1.dev1.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
+partis_bcr-1.0.11.post1.dev1.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
+partis_bcr-1.0.11.post1.dev1.data/scripts/partis-test.py,sha256=bQq_sT9v2DVQBgUGqQzdvy-q1jUrqAxV6Sl-tzENwus,63735
+partis_bcr-1.0.11.post1.dev1.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
+partis_bcr-1.0.11.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
@@ -373,7 +373,7 @@ 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=7sotd3b8qzZ7jcDFcVVHpxeozWuuLkrZdZApd_fiGDw,1859
+test/new-results/test.log,sha256=BIgsH4Lg5AHIReW5-dSXecZKFwUQY3gVs8XmzbGGEss,1858
 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
@@ -456,8 +456,8 @@ 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=1OOMLjMahLNNNKO_5-S9SnpiH4ep2t_SkGWMIr3yHVY,12599
-test/paired/new-results/run-times.csv,sha256=GcotLeK8Z5hWmBdyR9xNsE7f989cDWP01hu92Lupqlk,195
-test/paired/new-results/test.log,sha256=NXd8Tu0eTZFr_DByO507x6YPCYm4dlYAiohmfBqhpkg,72234
+test/paired/new-results/run-times.csv,sha256=E6L69mRYgMaicCUydybAsqulRy4jvKMVxHPi1R_BPbc,195
+test/paired/new-results/test.log,sha256=mZbbQkhUK0Nn8TZL0qd6Xn9TvZXlSIQqIrCwl1CML4s,72233
 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
@@ -472,23 +472,23 @@ 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=mqkth6pswWx75TJwW1dE_H2HQiy_d1ovFNDPJ6UlJmM,384
 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=qibHlOA04zulsDy_r0_-A5Bcq6-QBJQx_2E7W83yH7A,1546
+test/paired/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=M2bCQMx4ZfPcpj3_hKdcBCB73Atj6oiIEv6jlZN1Ejw,1546
 test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out,sha256=xmiiUt1hmQWLTOkbSt8J-9gsyE0sMhu0gNR1zxwUeDs,384
 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=l7l5uYqY2TA6xaTrGF4ulh9vxQNeVIcZ6D8R_VpvNt8,1547
+test/paired/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=yWdYpgimwYdiiirYSBx0Cl90YlUxlTMUP6f0RyErTtM,1547
 test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out,sha256=-7o36fTja9fprw6jh3E3wMWLrqED6yfDe8h-mSrVwGw,270
 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=-7Hbn-GBgPdmo9camyC3UxBmYfxxtRNXToTzvMZ2GqA,1547
+test/paired/new-results/partition-new-simu/fasttree/iclust-2/log,sha256=xBUFHMMTFoUEFe1ZGgST4jqxAm2fHfSBa_cV9xQptow,1547
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml,sha256=DeFoVNQJ3zbzSnuPsE8qoAvNSxalqTNYiWgyGZlV6hE,6135
 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=nnmC59opTanhhUFLO4Nz8BeKZvZ0QBr-oblRejb8eUo,4667
 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=fGk6KIDBUa5hk1-6aZQ7qCIhdU2eM-f4o6Y5hgx3v2Y,307
 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=JNYg4a7eN4SUvHPpcY1yTk2hgpagQ77H1whXEWj-AFg,1708
+test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log,sha256=JBfqHjWLBe73f0IdBjocazFAS_fcXW83tZ7hq5YAycE,1708
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out,sha256=Qy5GcANnwMQQ3RMail9Te4CcLtZm-QcECudLEMDlv3w,261
 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=98xOMgDgYhpzWd5YWKJNKzvVw7izjLEwSc1fp_R2FJU,1707
+test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log,sha256=LBAEPrhG0adTcUkhUMZ5r14S6ixJtz4GFNTP9Ork4kk,1707
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out,sha256=Y8lUkgKD485OevPo-Uvn4tA1qqOSyDyQqDeYxrenWIQ,178
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/input-seqs.fa,sha256=xmghMTcWRSKgyfKU2rnLHgIF5uDeVXOkQH2xOPKxo-o,2825
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log,sha256=RViVBnMIzWLyFzNukrjZzV5VF5ceEkEw3LcaA9CxH6U,1708
@@ -504,7 +504,7 @@ test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust
 test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log,sha256=P9TsoN4-YCijw5ITqARdQxb8Tx2jN4cFwY42KcW4KRA,1667
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/fasttree.out,sha256=NHP0OvZj0TMxkdx4P9ZYz596LdXSPERT_nOWjYExxL8,332
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/input-seqs.fa,sha256=bCiUVJqUAENg7ZjDOY14bKORc4OH2ZWA1b7JKeRykKw,3152
-test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log,sha256=amAo59kQ-FpvjMLP-L0wobFHaJfu1XGvSSG8KAo9zhI,1663
+test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log,sha256=m-k0tnJwBWXcyT7-ndxJ3uvVq3yAzech6sRklDNi5UU,1663
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/fasttree.out,sha256=nat74FqovsJB8XnyWZRGF1qNToiKUgi5biRMFKnmzWc,129
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/input-seqs.fa,sha256=m8dp3ZNW6yAGnUBEYLhA0m3ZRzG05GhMknB0qddZVqY,2450
 test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/log,sha256=5OmPmWuNFNj5TehA0-ZshzzvUBD74vZ5C6ELksQdJ9c,982
@@ -512,34 +512,34 @@ 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=5DYk3hChaUVJT7z3fLpGkgJiP-U5nBgMo9Y4YI32ikQ,29145
-test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg,sha256=tgSfStwAwG0Y8WaC1Ha7HPErtWkJ8ce7axX7C_8lLRY,22992
-test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg,sha256=3_jA0cRbC_aW-SVrqB8pjOV3e49JUc8ELYmdYTSQ3uI,19194
+test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg,sha256=AF1s9ql9zWt0zQ4iZrSu5WmH-1EDNCcKyMNCnKs53cY,29145
+test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg,sha256=U-dMbOQPDvsTrWGJH3BzJBfIfJt6mqDG5UrUfMmQtk4,22992
+test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg,sha256=PXTs7qKQfeambVlt6tFsgVlYOYkur8IlDiL7YDjyKog,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=AjXRJKEG6FmJx1V1L136m2BSD6B0YtK1aI8nqA8yJD4,7107
+test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg,sha256=sgFQ6Oe0uR7lH3xke5HvNMpQNRxtcb9I5r0gLV08Oyo,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=VbX4X9ARMVYrseRs5FlSbS0Ho1aBWFV8x6qtQco2KPg,8608
-test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg,sha256=bULet3Iycxh6rUtt8RXkEQdfBflQSgRuRGOYul4nTx4,13540
+test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg,sha256=2uc5EdmODArbpCLDbtTmM-q91c49I_f0gjfjbbSXa-Y,8608
+test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg,sha256=dNWrEtPW-FfIauVrLTNAqU5Bwql0T0Lb88pqn6-6rfs,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=rzgR8968Hn0vmw1HbvR6B1E0FCAW_5_wPT0K45mRseE,7763
+test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg,sha256=Dg5tqsF58c7A9EuMYCvWjJSWlnMPfPvUzmcnhwj55NU,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=tFUx9SHv2TB_d3VzWg1CG3maSHXbJ63PH71zgAGqswE,12644
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg,sha256=X9wYMpfczxXEIKNzWMO1hW_xTsZ5tsDBhlkuLF3WoOE,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=NfDnFTkq5b4i1VBhYNBBs1qmVDNIhoeQVSbXDANI0_U,12631
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg,sha256=1AoUvOnF9ntvoNdqKv6zCsMdTMabz8wDNsRHgZlZ8EE,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=HU0izHdIpWpENXoisR6ydlU2Co3a09hRyWaCIbjbvO8,12648
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg,sha256=U6mYZZQtDCys9AJqfQGHZPVtlmjXE-rsMeqL7diqiiY,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=caZ-BSMtoNaMzUsKqb2jwNUzAMLwVfHZN8mLCs1KIxc,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg,sha256=qB6a6BOPimDHt29qJVwxs7NY9O1n9nPWF8eH1SJxVkE,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=9xlANgX7w90UFBic3c0ku9JdEcdyOGFXHqLXgpuLcn0,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg,sha256=BMCnC-xfNH_KeQ00S087GswldyNGslo9XQkgyUb4ghw,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=0wZng0Y8AfoTeNsUV1uG_qGCqwjLdpgbmZdNOv1QOZ4,13482
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg,sha256=qVoUcIV9ApfcXijKr_z-dP2izdjY7XM-FZXUzpq2CAE,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=mT7GjllUgVh_in20cKHIS_ab-5BooM4qwsQQtLAZsoM,13931
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg,sha256=g0Fs7jIeb7w9URzN6Ky9BoPO59fkeR0p_y4tdJRfj2Q,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=Qgw-e5bfaPbpvJ0KAZvIb_r_p--tr5aHCX-Jinj4oMQ,9771
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=0_SoBRjTO5Rah4xYg0XV2Ul3jiziZKyk2cB6ivY2eXg,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
@@ -732,7 +732,7 @@ 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=RDbMsCDmgFCbxGGgCpo_Mf2L7d57-Yzu6fCbKkDhWqA,30272
+test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=TcsfYmaGb5LF5mHCwi18CGfPTkyxQgBw9l7r6qdr4KY,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
@@ -756,7 +756,7 @@ 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=IZmr3yBZ_LOqDdoFwFZBEsECkJNt_KqV38DHXtF43YI,24766
+test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=uDE9H_oajVVjd-1Ym8UWg6-EPMUJLYUWLuXYraAIMnQ,24766
 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
@@ -1107,7 +1107,7 @@ 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=CjHAnWyDZtOL-D2jB_Q0j0om0qtvEhrtZcoOSbk0gSg,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=lwdEtrZJSutvMUd7Yg_SmVQ0OL-TzSEavZUkd_trnSA,24714
+test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=ypMUJTGN1syhG_hg90-4EPPUjlyKpHPk4aLD_n43Gqc,24714
 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=mDDRdcCUT4gmdL5IQ1D2nGxXuTxdpEUvt83fNn1K35Q,27612
@@ -1476,7 +1476,7 @@ 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=hTAVrntmydr8n68pvMCakNE3twuuPUBrBJmeOgO3Wr4,140753
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=UvyynXa4XSglGh2b5htBnY-Dl-c8WLYGEVek311pCtE,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
@@ -1510,7 +1510,7 @@ 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=7VlZrXYAnRETAASjanMdREq_ursvwTBJYkzkUAI-BJY,78754
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=nDcz98p6nt7EWQwwXyl9zs4Keu167vPkO93844wxHcU,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
@@ -1529,7 +1529,7 @@ 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=FCyBdqRVa6_rzcTFgMMYUKfnQMWoQMHfgwhmxz-eQ_U,44439
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=GsxUJUspmQpWaqTRFOqItdOwBT9C_5yZaut5vDTz9s8,44439
 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
@@ -7899,8 +7899,8 @@ 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.post1.dev1.dist-info/METADATA,sha256=1Pd16fi8-YN5QIP2EEA5MIiNP5UkbT9dC1XeczkBNsg,5019
-partis_bcr-1.0.10.post1.dev1.dist-info/WHEEL,sha256=_N1vyLgwJ10g4JxFsp-IfU42zGJgf-DUqwfdbV1YvEM,115
-partis_bcr-1.0.10.post1.dev1.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.10.post1.dev1.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.10.post1.dev1.dist-info/RECORD,,
+partis_bcr-1.0.11.post1.dev1.dist-info/METADATA,sha256=6ShzvolO4EwZl-P13LVatUIlWpy837twI_X-taZO3fU,5019
+partis_bcr-1.0.11.post1.dev1.dist-info/WHEEL,sha256=_N1vyLgwJ10g4JxFsp-IfU42zGJgf-DUqwfdbV1YvEM,115
+partis_bcr-1.0.11.post1.dev1.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.11.post1.dev1.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.11.post1.dev1.dist-info/RECORD,,

test/new-results/test.log

@@ -1,22 +1,22 @@
 cache-parameters-quick-new-simu   partis cache-parameters --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 --n-max-queries 10 --random-seed 1 --n-procs 10
   --n-max-queries: stopped after reading 10 queries from input file
 caching parameters
-  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.1 sec
+  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.0 sec
     keeping 2 / 198 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.2 sec
+  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.1 sec
     running 10 procs for 10 seqs
       info for 10 / 10 = 1.000   (removed: 0 failed)
       kept 10 (1.000) unproductive
     water time: 0.2  (ig-sw 0.0  processing 0.2)
 smith-waterman  (writing parameters)
-  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.2 sec
+  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.1 sec
     running 10 procs for 10 seqs
       info for 10 / 10 = 1.000   (removed: 0 failed)
       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 (8.6 sec)
-    water time: 8.8  (ig-sw 8.6  processing 0.2)
+    writing parameters to test/new-results/test/parameters/simu/sw (2.0 sec)
+    water time: 2.2  (ig-sw 2.0  processing 0.1)
   writing hmms     removed 35 genes from glfo (leaving v 2  d 1  j 2)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
@@ -24,11 +24,11 @@ smith-waterman  (writing parameters)
 hmm
     reading output
         read 10 hmm output lines with 10 sequences in 10 events  (0 failures)
-    writing parameters to test/new-results/test/parameters/simu/hmm (0.4 sec)
-         infra time: 0.6
-      hmm step time: 1.6
+    writing parameters to test/new-results/test/parameters/simu/hmm (0.2 sec)
+         infra time: 0.3
+      hmm step time: 0.6
   writing hmms     removed 0  genes from glfo (leaving v 2  d 1  j 2)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.3 sec)
-      total time: 11.6
+(0.2 sec)
+      total time: 3.6

test/paired/new-results/partition-new-simu/fasttree/iclust-0/log

@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
 Ignored unknown character X (seen 32 times)
 Initial topology in 0.00 seconds
 Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
-Total branch-length 0.172 after 0.01 sec
+Total branch-length 0.172 after 0.00 sec
 ML-NNI round 1: LogLk = -1718.230 NNIs 0 max delta 0.00 Time 0.01
 GTR Frequencies: 0.2101 0.3021 0.2760 0.2118
 GTR rates(ac ag at cg ct gt) 1.2927 1.2254 1.4006 0.7465 1.0327 1.0000
@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.666 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1660.926 NNIs 0 max delta 0.00 Time 0.04
+ML-NNI round 2: LogLk = -1660.926 NNIs 0 max delta 0.00 Time 0.03
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.05 (final)
+ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.04 (final)
 Optimize all lengths: LogLk = -1660.925 Time 0.05
-Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5
+Total time: 0.06 seconds Unique: 8/8 Bad splits: 0/5

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

@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
 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
+Total branch-length 0.116 after 0.00 sec
 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) 0.7182 0.4393 0.9759 0.8068 0.8119 1.0000
@@ -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 = -1478.012 NNIs 0 max delta 0.00 Time 0.04
+ML-NNI round 2: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.03
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.05 (final)
-Optimize all lengths: LogLk = -1478.012 Time 0.06
-Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.04 (final)
+Optimize all lengths: LogLk = -1478.012 Time 0.04
+Total time: 0.06 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/fasttree/iclust-2/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.641 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 = -1274.638 NNIs 0 max delta 0.00 Time 0.03
+ML-NNI round 2: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.04 (final)
-Optimize all lengths: LogLk = -1274.638 Time 0.04
-Total time: 0.05 seconds Unique: 6/6 Bad splits: 0/3
+ML-NNI round 3: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.03 (final)
+Optimize all lengths: LogLk = -1274.638 Time 0.03
+Total time: 0.04 seconds Unique: 6/6 Bad splits: 0/3

test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.678 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 = -968.458 NNIs 0 max delta 0.00 Time 0.03
+ML-NNI round 2: LogLk = -968.458 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -968.419 NNIs 0 max delta 0.00 Time 0.04 (final)
-Optimize all lengths: LogLk = -968.417 Time 0.04
-Total time: 0.06 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -968.419 NNIs 0 max delta 0.00 Time 0.03 (final)
+Optimize all lengths: LogLk = -968.417 Time 0.03
+Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/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 = -794.353 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -794.321 NNIs 0 max delta 0.00 Time 0.03 (final)
-Optimize all lengths: LogLk = -794.321 Time 0.03
-Total time: 0.04 seconds Unique: 7/7 Bad splits: 0/4
+ML-NNI round 3: LogLk = -794.321 NNIs 0 max delta 0.00 Time 0.02 (final)
+Optimize all lengths: LogLk = -794.321 Time 0.02
+Total time: 0.03 seconds Unique: 7/7 Bad splits: 0/4

test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log

@@ -17,6 +17,6 @@ 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 = -613.260 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.03 (final)
-Optimize all lengths: LogLk = -613.260 Time 0.03
-Total time: 0.04 seconds Unique: 8/9 Bad splits: 0/5
+ML-NNI round 3: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.02 (final)
+Optimize all lengths: LogLk = -613.260 Time 0.02
+Total time: 0.03 seconds Unique: 8/9 Bad splits: 0/5