partis-bcr 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev7__cp312-cp312-manylinux1_x86_64.whl

python/recombinator.py

@@ -721,6 +721,7 @@ class Recombinator(object):
 
         full_seq = reco_event.recombined_seq
         if not self.args.no_per_base_mutation:
+            print('      using bpp per-base mutation with path %s' % bpp_path)
             paramfname = workdir + '/cfg.bpp'  # docs: http://biopp.univ-montp2.fr/apidoc/bpp-phyl/html/index.html that page is too darn hard to google
             workfnames.append(paramfname)
             plines = ['alphabet = DNA']
@@ -774,6 +775,7 @@ class Recombinator(object):
                 pfile.write('\n'.join(plines))
             command = '%s param=%s --seed=%d' % (bpp_binary, paramfname, seed)  # not sure how to set the seed in the param file, but this works, so oh well
         else:
+            print('      using bpp uniform mutation with path %s' % bpp_path)
             command = bpp_binary  # NOTE should I use the "equilibrium frequencies" option?
             command += ' alphabet=DNA'
             command += ' --seed=' + str(seed)

python/treegenerator.py

@@ -204,7 +204,7 @@ class TreeGenerator(object):
                 os.remove(outfname)
             utils.run_r(cmd_lines, workdir, print_time='tree generation' if self.args.debug else None, remove_cmdfile=True)
 
-        with open(outfname) as treefile:
+        with open(outfname) as treefile:  # NOTE atm <outfname> by default is .yaml (set in recombinator.py) since it later gets used as yaml, but stupidly here we temporarily use it as a multi-line nwk here (since, here, it used to be nwk), but don't want to change atm since it's invisible and internal and works fine
             for itree, tstr in enumerate(treestrs):
                 if tstr is None:
                     treestrs[itree] = treefile.readline().strip()

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv

@@ -0,0 +1,7 @@
+bin_low_edge,contents,binlabel,error
+-3.5,0.0,,0.0
+-2.5,7.0,,2.6457513110645907
+-1.5,2,,1.4142135623730951
+-0.5,25,,5.0
+0.5,1.0,,1.0
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv

@@ -0,0 +1,8 @@
+bin_low_edge,contents,binlabel,error
+-3.5,0.0,,0.0
+-2.5,3.0,,1.7320508075688772
+-1.5,0.0,,0.0
+-0.5,30,,5.477225575051661
+0.5,1,,1.0
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv

@@ -0,0 +1,8 @@
+bin_low_edge,contents,binlabel,error
+-4.5,0.0,,0.0
+-3.5,8.0,,2.8284271247461903
+-2.5,4,,2.0
+-1.5,2,,1.4142135623730951
+-0.5,19,,4.358898943540674
+0.5,2.0,,1.4142135623730951
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv

@@ -0,0 +1,10 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,7.0,,2.6457513110645907
+0.5,0.0,,0.0
+1.5,0.0,,0.0
+2.5,13,,3.605551275463989
+3.5,0.0,,0.0
+4.5,0.0,,0.0
+5.5,15.0,,3.872983346207417
+6.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv

@@ -0,0 +1,8 @@
+bin_low_edge,contents,binlabel,error
+-4.5,0.0,,0.0
+-3.5,1.0,,1.0
+-2.5,3,,1.7320508075688772
+-1.5,7,,2.6457513110645907
+-0.5,22,,4.69041575982343
+0.5,2.0,,1.4142135623730951
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv

@@ -0,0 +1,8 @@
+bin_low_edge,contents,binlabel,error
+-5.5,0.0,,0.0
+-4.5,1.0,,1.0
+-3.5,0.0,,0.0
+-2.5,0.0,,0.0
+-1.5,0.0,,0.0
+-0.5,3.0,,1.7320508075688772
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv

@@ -0,0 +1,8 @@
+bin_low_edge,contents,binlabel,error
+-3.5,0.0,,0.0
+-2.5,3.0,,1.7320508075688772
+-1.5,0.0,,0.0
+-0.5,30,,5.477225575051661
+0.5,1,,1.0
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.04,0.0,,0.0
+0.0,0.0,,0.0
+0.04,0.0,,0.0
+0.08,0.0,,0.0
+0.12,0.0,,0.0
+0.16,0.0,,0.0
+0.2,0.0,,0.0
+0.24,0.0,,0.0
+0.28,0.0,,0.0
+0.32,0.0,,0.0
+0.36,0.0,,0.0
+0.4,0.0,,0.0
+0.44,0.0,,0.0
+0.48,0.0,,0.0
+0.52,0.0,,0.0
+0.56,0.0,,0.0
+0.6,0.0,,0.0
+0.64,0.0,,0.0
+0.68,0.0,,0.0
+0.72,0.0,,0.0
+0.76,0.0,,0.0
+0.8,0.0,,0.0
+0.84,0.0,,0.0
+0.88,0.0,,0.0
+0.92,0.0,,0.0
+0.96,0.0,,0.0
+1.0,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.016,0.0,,0.0
+0.0,0.9642857142857143,,0.08201246007278784
+0.016,1.0,,0.12831445712826428
+0.032,0.0,,0.0
+0.048,0.0,,0.0
+0.064,0.0,,0.0
+0.08,0.0,,0.0
+0.096,0.0,,0.0
+0.112,0.0,,0.0
+0.128,0.0,,0.0
+0.14400000000000002,0.0,,0.0
+0.16,0.0,,0.0
+0.176,0.0,,0.0
+0.192,0.0,,0.0
+0.20800000000000002,0.0,,0.0
+0.224,0.0,,0.0
+0.24,0.0,,0.0
+0.256,0.0,,0.0
+0.272,0.0,,0.0
+0.28800000000000003,0.0,,0.0
+0.304,0.0,,0.0
+0.32,0.0,,0.0
+0.336,0.0,,0.0
+0.352,0.0,,0.0
+0.368,0.0,,0.0
+0.384,0.0,,0.0
+0.4,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,0.9714285714285714,right,0.058548549035571384
+0.5,0.02857142857142857,wrong,0.058548549035571426
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.04,0.0,,0.0
+0.0,0.0,,0.0
+0.04,0.0,,0.0
+0.08,0.0,,0.0
+0.12,0.0,,0.0
+0.16,0.0,,0.0
+0.2,0.0,,0.0
+0.24,0.0,,0.0
+0.28,0.0,,0.0
+0.32,0.0,,0.0
+0.36,0.0,,0.0
+0.4,0.0,,0.0
+0.44,0.0,,0.0
+0.48,0.0,,0.0
+0.52,0.0,,0.0
+0.56,0.0,,0.0
+0.6,0.0,,0.0
+0.64,0.0,,0.0
+0.68,0.0,,0.0
+0.72,0.0,,0.0
+0.76,0.0,,0.0
+0.8,0.0,,0.0
+0.84,0.0,,0.0
+0.88,0.0,,0.0
+0.92,0.0,,0.0
+0.96,0.0,,0.0
+1.0,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.016,0.0,,0.0
+0.0,1.0,,0.03717459069360163
+0.016,1.0,,0.12831445712826428
+0.032,0.0,,0.0
+0.048,0.0,,0.0
+0.064,0.0,,0.0
+0.08,0.0,,0.0
+0.096,0.0,,0.0
+0.112,0.0,,0.0
+0.128,0.0,,0.0
+0.14400000000000002,0.0,,0.0
+0.16,0.0,,0.0
+0.176,0.0,,0.0
+0.192,0.0,,0.0
+0.20800000000000002,0.0,,0.0
+0.224,0.0,,0.0
+0.24,0.0,,0.0
+0.256,0.0,,0.0
+0.272,0.0,,0.0
+0.28800000000000003,0.0,,0.0
+0.304,0.0,,0.0
+0.32,0.0,,0.0
+0.336,0.0,,0.0
+0.352,0.0,,0.0
+0.368,0.0,,0.0
+0.384,0.0,,0.0
+0.4,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,1.0,right,0.030056064897528434
+0.5,0.0,wrong,0.066735136327
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.04,0.0,,0.0
+0.0,0.0,,0.0
+0.04,0.0,,0.0
+0.08,0.0,,0.0
+0.12,0.0,,0.0
+0.16,0.0,,0.0
+0.2,0.0,,0.0
+0.24,0.0,,0.0
+0.28,0.0,,0.0
+0.32,0.0,,0.0
+0.36,0.0,,0.0
+0.4,0.0,,0.0
+0.44,0.0,,0.0
+0.48,0.0,,0.0
+0.52,0.0,,0.0
+0.56,0.0,,0.0
+0.6,0.0,,0.0
+0.64,0.0,,0.0
+0.68,0.0,,0.0
+0.72,0.0,,0.0
+0.76,0.0,,0.0
+0.8,0.0,,0.0
+0.84,0.0,,0.0
+0.88,0.0,,0.0
+0.92,0.0,,0.0
+0.96,0.0,,0.0
+1.0,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.016,0.0,,0.0
+0.0,1.0,,0.03717459069360163
+0.016,1.0,,0.12831445712826428
+0.032,0.0,,0.0
+0.048,0.0,,0.0
+0.064,0.0,,0.0
+0.08,0.0,,0.0
+0.096,0.0,,0.0
+0.112,0.0,,0.0
+0.128,0.0,,0.0
+0.14400000000000002,0.0,,0.0
+0.16,0.0,,0.0
+0.176,0.0,,0.0
+0.192,0.0,,0.0
+0.20800000000000002,0.0,,0.0
+0.224,0.0,,0.0
+0.24,0.0,,0.0
+0.256,0.0,,0.0
+0.272,0.0,,0.0
+0.28800000000000003,0.0,,0.0
+0.304,0.0,,0.0
+0.32,0.0,,0.0
+0.336,0.0,,0.0
+0.352,0.0,,0.0
+0.368,0.0,,0.0
+0.384,0.0,,0.0
+0.4,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,1.0,right,0.030056064897528434
+0.5,0.0,wrong,0.066735136327
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv

@@ -0,0 +1,7 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,30.0,,5.477225575051661
+0.5,2,,1.4142135623730951
+1.5,2,,1.4142135623730951
+2.5,1.0,,1.0
+3.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv

@@ -0,0 +1,7 @@
+bin_low_edge,contents,binlabel,error
+-2.5,0.0,,0.0
+-1.5,1.0,,1.0
+-0.5,30,,5.477225575051661
+0.5,2,,1.4142135623730951
+1.5,2.0,,1.4142135623730951
+2.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,34.0,,5.830951894845301
+0.5,1.0,,1.0
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv

@@ -0,0 +1,6 @@
+bin_low_edge,contents,binlabel,error
+-2.5,0.0,,0.0
+-1.5,1.0,,1.0
+-0.5,31,,5.5677643628300215
+0.5,3.0,,1.7320508075688772
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv

@@ -0,0 +1,7 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,30.0,,5.477225575051661
+0.5,2,,1.4142135623730951
+1.5,2,,1.4142135623730951
+2.5,1.0,,1.0
+3.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,31.0,,5.5677643628300215
+0.5,4.0,,2.0
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.0432,0.0,,0.0
+-0.04,0.0,,0.0
+-0.0368,0.0,,0.0
+-0.0336,0.0,,0.0
+-0.0304,0.0,,0.0
+-0.027200000000000002,0.0,,0.0
+-0.024,0.0,,0.0
+-0.0208,0.0,,0.0
+-0.0176,0.0,,0.0
+-0.0144,0.0,,0.0
+-0.011199999999999998,0.0,,0.0
+-0.008,0.0,,0.0
+-0.004799999999999999,1.0,,1.0
+-0.0015999999999999973,30.0,,5.477225575051661
+0.0016000000000000042,2.0,,1.4142135623730951
+0.004799999999999999,2.0,,1.4142135623730951
+0.008,0.0,,0.0
+0.011200000000000002,0.0,,0.0
+0.014400000000000003,0.0,,0.0
+0.017600000000000005,0.0,,0.0
+0.0208,0.0,,0.0
+0.024,0.0,,0.0
+0.02720000000000001,0.0,,0.0
+0.030400000000000003,0.0,,0.0
+0.0336,0.0,,0.0
+0.036800000000000006,0.0,,0.0
+0.04,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv

@@ -0,0 +1,7 @@
+bin_low_edge,contents,binlabel,error
+-2.5,0.0,,0.0
+-1.5,1.0,,1.0
+-0.5,30,,5.477225575051661
+0.5,2,,1.4142135623730951
+1.5,2.0,,1.4142135623730951
+2.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv

@@ -0,0 +1,8 @@
+bin_low_edge,contents,binlabel,error
+-3.5,0.0,,0.0
+-2.5,7.0,,2.6457513110645907
+-1.5,2,,1.4142135623730951
+-0.5,24,,4.898979485566356
+0.5,1,,1.0
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv

@@ -0,0 +1,6 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,33.0,,5.744562646538029
+0.5,1,,1.0
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv

@@ -0,0 +1,7 @@
+bin_low_edge,contents,binlabel,error
+-4.5,0.0,,0.0
+-3.5,9.0,,3.0
+-2.5,1,,1.0
+-1.5,2,,1.4142135623730951
+-0.5,23.0,,4.795831523312719
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv

@@ -0,0 +1,9 @@
+bin_low_edge,contents,binlabel,error
+-6.5,0.0,,0.0
+-5.5,1.0,,1.0
+-4.5,0.0,,0.0
+-3.5,1,,1.0
+-2.5,0.0,,0.0
+-1.5,7,,2.6457513110645907
+-0.5,26.0,,5.0990195135927845
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv

@@ -0,0 +1,8 @@
+bin_low_edge,contents,binlabel,error
+-5.5,0.0,,0.0
+-4.5,1.0,,1.0
+-3.5,0.0,,0.0
+-2.5,0.0,,0.0
+-1.5,0.0,,0.0
+-0.5,3.0,,1.7320508075688772
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv

@@ -0,0 +1,4 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,35.0,,5.916079783099616
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv

@@ -0,0 +1,6 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,33.0,,5.744562646538029
+0.5,1,,1.0
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.016,0.0,,0.0
+0.0,0.9642857142857143,,0.08201246007278784
+0.016,1.0,,0.12831445712826428
+0.032,0.0,,0.0
+0.048,0.0,,0.0
+0.064,0.0,,0.0
+0.08,0.0,,0.0
+0.096,0.0,,0.0
+0.112,0.0,,0.0
+0.128,0.0,,0.0
+0.14400000000000002,0.0,,0.0
+0.16,0.0,,0.0
+0.176,0.0,,0.0
+0.192,0.0,,0.0
+0.20800000000000002,0.0,,0.0
+0.224,0.0,,0.0
+0.24,0.0,,0.0
+0.256,0.0,,0.0
+0.272,0.0,,0.0
+0.28800000000000003,0.0,,0.0
+0.304,0.0,,0.0
+0.32,0.0,,0.0
+0.336,0.0,,0.0
+0.352,0.0,,0.0
+0.368,0.0,,0.0
+0.384,0.0,,0.0
+0.4,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,0.9714285714285714,right,0.058548549035571384
+0.5,0.02857142857142857,wrong,0.058548549035571426
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.016,0.0,,0.0
+0.0,1.0,,0.03717459069360163
+0.016,1.0,,0.12831445712826428
+0.032,0.0,,0.0
+0.048,0.0,,0.0
+0.064,0.0,,0.0
+0.08,0.0,,0.0
+0.096,0.0,,0.0
+0.112,0.0,,0.0
+0.128,0.0,,0.0
+0.14400000000000002,0.0,,0.0
+0.16,0.0,,0.0
+0.176,0.0,,0.0
+0.192,0.0,,0.0
+0.20800000000000002,0.0,,0.0
+0.224,0.0,,0.0
+0.24,0.0,,0.0
+0.256,0.0,,0.0
+0.272,0.0,,0.0
+0.28800000000000003,0.0,,0.0
+0.304,0.0,,0.0
+0.32,0.0,,0.0
+0.336,0.0,,0.0
+0.352,0.0,,0.0
+0.368,0.0,,0.0
+0.384,0.0,,0.0
+0.4,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,1.0,right,0.030056064897528434
+0.5,0.0,wrong,0.066735136327
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv

@@ -0,0 +1,28 @@
+bin_low_edge,contents,binlabel,error
+-0.016,0.0,,0.0
+0.0,1.0,,0.03717459069360163
+0.016,1.0,,0.12831445712826428
+0.032,0.0,,0.0
+0.048,0.0,,0.0
+0.064,0.0,,0.0
+0.08,0.0,,0.0
+0.096,0.0,,0.0
+0.112,0.0,,0.0
+0.128,0.0,,0.0
+0.14400000000000002,0.0,,0.0
+0.16,0.0,,0.0
+0.176,0.0,,0.0
+0.192,0.0,,0.0
+0.20800000000000002,0.0,,0.0
+0.224,0.0,,0.0
+0.24,0.0,,0.0
+0.256,0.0,,0.0
+0.272,0.0,,0.0
+0.28800000000000003,0.0,,0.0
+0.304,0.0,,0.0
+0.32,0.0,,0.0
+0.336,0.0,,0.0
+0.352,0.0,,0.0
+0.368,0.0,,0.0
+0.384,0.0,,0.0
+0.4,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,1.0,right,0.030056064897528434
+0.5,0.0,wrong,0.066735136327
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv

@@ -0,0 +1,6 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,31.0,,5.5677643628300215
+0.5,3,,1.7320508075688772
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv

@@ -0,0 +1,7 @@
+bin_low_edge,contents,binlabel,error
+-2.5,0.0,,0.0
+-1.5,2.0,,1.4142135623730951
+-0.5,31,,5.5677643628300215
+0.5,1,,1.0
+1.5,1.0,,1.0
+2.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,34.0,,5.830951894845301
+0.5,1.0,,1.0
+1.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv

@@ -0,0 +1,5 @@
+bin_low_edge,contents,binlabel,error
+-2.5,0.0,,0.0
+-1.5,1.0,,1.0
+-0.5,34.0,,5.830951894845301
+0.5,0.0,,0.0

test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv

@@ -0,0 +1,6 @@
+bin_low_edge,contents,binlabel,error
+-1.5,0.0,,0.0
+-0.5,31.0,,5.5677643628300215
+0.5,3,,1.7320508075688772
+1.5,1.0,,1.0
+2.5,0.0,,0.0