partis-bcr 1.0.8__py3-none-any.whl → 1.0.9.post1.dev1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- packages/ham/bcrham +0 -0
- packages/ig-sw/src/ig_align/ig-sw +0 -0
- {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/METADATA +1 -1
- {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/RECORD +155 -73
- test/new-results/get-selection-metrics-new-simu.yaml +1 -0
- test/new-results/test.log +12 -16
- test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv +8 -8
- test/paired/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -1
- test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +8 -8
- test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -1
- test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +7 -7
- test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -1
- test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +9 -9
- test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/fasttree.out +1 -1
- test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +8 -8
- test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out +1 -1
- test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +9 -9
- test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml +1 -1
- test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out +1 -1
- test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +8 -8
- test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/fasttree.out +1 -1
- test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/log +4 -4
- test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metrics.yaml +1 -1
- test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/fasttree.out +1 -1
- test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +9 -9
- test/paired/new-results/partition-new-simu/igh+igl/partition-igh-selection-metrics.yaml +1 -1
- test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/fasttree.out +1 -1
- test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +9 -9
- test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/log +3 -3
- test/paired/new-results/partition-new-simu/igh+igl/partition-igl-selection-metrics.yaml +1 -1
- test/paired/new-results/partition-new-simu/selection-metrics.yaml +1 -1
- test/paired/new-results/partition-new-simu/single-chain/partition-igh.yaml +1 -1
- test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
- test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
- test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
- test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
- test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
- test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
- test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
- test/paired/new-results/run-times.csv +6 -6
- test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +86 -102
- test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/isub-1/partition-igh.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +84 -100
- test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igh.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-partition.log +50 -54
- test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partition-igh.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igh.yaml +1 -1
- test/paired/new-results/test.log +203 -236
- test/ref-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
- test/ref-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
- test/ref-results/partition-new-simu/fasttree/iclust-0/log +23 -0
- test/ref-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
- test/ref-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
- test/ref-results/partition-new-simu/fasttree/iclust-1/log +23 -0
- test/ref-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
- test/ref-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
- test/ref-results/partition-new-simu/fasttree/iclust-2/log +22 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/input-seqs.fa +24 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/log +430 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.bionj +1 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.ckp.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.iqtree +282 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.log +429 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.mldist +13 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.model.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.state +3529 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile +1 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa +16 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/log +373 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.bionj +1 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.ckp.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree +279 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.log +372 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.mldist +9 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.state +2229 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile +1 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa +16 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/log +375 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.bionj +1 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.ckp.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree +274 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.log +374 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.mldist +9 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.state +2283 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile +1 -0
- test/ref-results/partition-new-simu/iqtree-annotations.yaml +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa +24 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralProbs +3461 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralStates +10 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestModel +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTree +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log +216 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.mlTrees +20 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.rba +0 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.reduced.phy +9 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.startTree +20 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/log +454 -0
- test/ref-results/partition-new-simu/raxml/iclust-0/run.sh +3 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa +16 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralProbs +2203 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralStates +6 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestModel +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTree +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log +217 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.mlTrees +20 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.rba +0 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.reduced.phy +4 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.startTree +20 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/log +440 -0
- test/ref-results/partition-new-simu/raxml/iclust-1/run.sh +3 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa +16 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs +2275 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates +6 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestModel +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTree +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log +207 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.mlTrees +20 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.rba +0 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.startTree +20 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/log +420 -0
- test/ref-results/partition-new-simu/raxml/iclust-2/run.sh +3 -0
- test/ref-results/partition-new-simu/raxml-annotations.yaml +1 -0
- bin/FastTree-macos +0 -0
- {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-alleles.py +0 -0
- {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-germlines.py +0 -0
- {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
- {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
- {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/gctree-run.py +0 -0
- {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
- {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/parse-output.py +0 -0
- {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/partis-test.py +0 -0
- {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/split-loci.py +0 -0
- {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/WHEEL +0 -0
- {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/entry_points.txt +0 -0
- {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/licenses/COPYING +0 -0
- {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/top_level.txt +0 -0
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# Ancestral state reconstruction for all nodes in /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile
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# This file can be read in MS Excel or in R with command:
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# tab=read.table('/home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.state',header=TRUE)
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# Columns are tab-separated with following meaning:
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# Node: Node name in the tree
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# Site: Alignment site ID
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# State: Most likely state assignment
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# p_X: Posterior probability for state X (empirical Bayesian method)
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Node Site State p_A p_C p_G p_T
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Node4 1 C 0.00000 1.00000 0.00000 0.00000
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Node4 2 A 1.00000 0.00000 0.00000 0.00000
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Node4 3 G 0.00000 0.00000 1.00000 0.00000
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Node4 4 G 0.00000 0.00000 1.00000 0.00000
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Node4 5 T 0.00000 0.00000 0.00000 1.00000
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Node4 6 G 0.00000 0.00000 1.00000 0.00000
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Node4 7 C 0.00000 1.00000 0.00000 0.00000
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Node4 8 A 1.00000 0.00000 0.00000 0.00000
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Node4 9 G 0.00000 0.00000 1.00000 0.00000
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Node4 10 C 0.00000 1.00000 0.00000 0.00000
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Node4 11 T 0.00000 0.00000 0.00000 1.00000
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Node4 12 G 0.00000 0.00000 1.00000 0.00000
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Node4 13 C 0.00000 1.00000 0.00000 0.00000
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Node4 14 A 1.00000 0.00000 0.00000 0.00000
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Node4 15 G 0.00000 0.00000 1.00000 0.00000
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Node4 16 G 0.00000 0.00000 1.00000 0.00000
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Node4 17 A 1.00000 0.00000 0.00000 0.00000
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Node4 18 G 0.00000 0.00000 1.00000 0.00000
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Node4 19 T 0.00000 0.00000 0.00000 1.00000
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Node4 20 C 0.00000 1.00000 0.00000 0.00000
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Node4 21 G 0.00000 0.00000 1.00000 0.00000
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Node4 22 G 0.00000 0.00000 1.00000 0.00000
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Node4 23 G 0.00000 0.00000 1.00000 0.00000
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Node4 24 C 0.00000 1.00000 0.00000 0.00000
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Node4 25 C 0.00000 1.00000 0.00000 0.00000
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Node4 26 C 0.00000 1.00000 0.00000 0.00000
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Node4 27 A 1.00000 0.00000 0.00000 0.00000
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Node4 28 G 0.00000 0.00000 1.00000 0.00000
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Node4 29 G 0.00000 0.00000 1.00000 0.00000
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Node4 30 A 1.00000 0.00000 0.00000 0.00000
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Node4 31 C 0.00000 1.00000 0.00000 0.00000
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Node4 32 T 0.00000 0.00000 0.00000 1.00000
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Node4 33 G 0.00000 0.00000 1.00000 0.00000
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Node4 34 G 0.00000 0.00000 1.00000 0.00000
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Node4 35 T 0.00000 0.00000 0.00000 1.00000
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Node4 36 G 0.00000 0.00000 1.00000 0.00000
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Node4 37 A 1.00000 0.00000 0.00000 0.00000
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Node4 38 A 1.00000 0.00000 0.00000 0.00000
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Node4 39 G 0.00000 0.00000 1.00000 0.00000
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Node4 40 C 0.00000 1.00000 0.00000 0.00000
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Node4 41 C 0.00000 1.00000 0.00000 0.00000
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Node4 42 T 0.00000 0.00000 0.00000 1.00000
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Node4 43 T 0.00000 0.00000 0.00000 1.00000
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Node4 44 C 0.00000 1.00000 0.00000 0.00000
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Node4 45 G 0.00000 0.00000 1.00000 0.00000
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Node4 46 G 0.00000 0.00000 1.00000 0.00000
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Node4 47 A 1.00000 0.00000 0.00000 0.00000
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Node4 48 G 0.00000 0.00000 1.00000 0.00000
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Node4 49 A 1.00000 0.00000 0.00000 0.00000
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Node4 50 C 0.00000 1.00000 0.00000 0.00000
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Node4 51 C 0.00000 1.00000 0.00000 0.00000
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Node4 52 C 0.00000 1.00000 0.00000 0.00000
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Node4 53 T 0.00000 0.00000 0.00000 1.00000
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Node4 54 G 0.00000 0.00000 1.00000 0.00000
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Node4 55 T 0.00000 0.00000 0.00000 1.00000
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Node4 56 C 0.00000 1.00000 0.00000 0.00000
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Node4 57 C 0.00000 1.00000 0.00000 0.00000
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Node4 58 C 0.00000 1.00000 0.00000 0.00000
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