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issues with handling one sample at low coverage #46

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murphycj2 opened this issue Jun 10, 2021 · 0 comments · Fixed by #47
Closed

issues with handling one sample at low coverage #46

murphycj2 opened this issue Jun 10, 2021 · 0 comments · Fixed by #47
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@murphycj2
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WARNING - 2021-06-10 19:09:47,430: You should specify 2 or more samples in order to compare genotypes.
	INFO - 2021-06-10 19:09:47,499: Total comparisons: 1
	INFO - 2021-06-10 19:09:47,502: Count of expected matches: 0
	INFO - 2021-06-10 19:09:47,503: Count of unexpected matches: 0
	INFO - 2021-06-10 19:09:47,504: Count of unexpected mismatches: 1
	INFO - 2021-06-10 19:09:47,505: Count of expected mismatches: 0
	INFO - 2021-06-10 19:09:47,513: Clustering input samples...
	Traceback (most recent call last):
	  File "/usr/local/bin/biometrics", line 8, in <module>
	    sys.exit(main())
	  File "/usr/local/lib/python3.6/site-packages/biometrics/cli.py", line 252, in main
	    run_biometrics(args)
	  File "/usr/local/lib/python3.6/site-packages/biometrics/biometrics.py", line 412, in run_biometrics
	    run_genotyping(args, samples)
	  File "/usr/local/lib/python3.6/site-packages/biometrics/biometrics.py", line 144, in run_genotyping
	    clusters = cluster_handler.cluster(comparisons_input)
	  File "/usr/local/lib/python3.6/site-packages/biometrics/cluster.py", line 81, in cluster
	    len(sample2group), cluster_idx + 1, len(set(clusters['expected_sample_group']))))
	UnboundLocalError: local variable 'cluster_idx' referenced before assignment
	Traceback (most recent call last):
	  File "/usr/local/bin/biometrics", line 8, in <module>
	    sys.exit(main())
	  File "/usr/local/lib/python3.6/site-packages/biometrics/cli.py", line 252, in main
	    run_biometrics(args)
	  File "/usr/local/lib/python3.6/site-packages/biometrics/biometrics.py", line 406, in run_biometrics
	    run_minor_contamination(args, samples)
	  File "/usr/local/lib/python3.6/site-packages/biometrics/biometrics.py", line 81, in run_minor_contamination
	    minor_contamination.plot(samples, args.outdir)
	  File "/usr/local/lib/python3.6/site-packages/biometrics/minor_contamination.py", line 78, in plot
	    if len(contributing_sites) > 0:
	TypeError: object of type 'float' has no len()
@murphycj2 murphycj2 added the bug Something isn't working label Jun 10, 2021
@murphycj2 murphycj2 self-assigned this Jun 10, 2021
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