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obi clean: fixed a memory bug, fixed the behaviour when no sample info,

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and added checks warnings and error handling when sample info not
dereplicated
This commit is contained in:
Celine Mercier
2020-07-01 18:17:47 +02:00
parent ade1107b42
commit aab59f2214
4 changed files with 25 additions and 8 deletions
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6
python/obitools3/commands/clean.pyx
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@ -36,8 +36,7 @@ def addOptions(parser):
dest="clean:sample-tag-name",
metavar="<SAMPLE TAG NAME>",
type=str,
default="merged_sample",
help="Name of the tag where sample counts are kept.")
help="Name of the tag where merged sample count informations are kept (typically generated by obi uniq, usually MERGED_sample, default: None).")
group.add_argument('--ratio', '-r',
action="store", dest="clean:ratio",
@ -107,6 +106,9 @@ def run(config):
command_line = " ".join(sys.argv[1:])
comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
if 'sample-tag-name' not in config['clean']:
config['clean']['sample-tag-name'] = ""
if obi_clean(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], config['clean']['thread-count']) < 0:
raise Exception("Error running obiclean")