-
--add-exon-ids
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--add-missing-ids
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--clean
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--clean-exclude-attributes
-
--clean-group-sgds
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--clean-replace-attributes
-
--clean-score
-
--debug
-
--discard-unresolved
-
--fields=FIELD_LIST
-
--gff
-
--htseq-count
-
--insert-missing=GENE_FILE
-
--no-percent-encoding
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-
--prepend=PREPEND_STR
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--remove-attribute=RM_ATTR
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--report-duplicates
-
--resolve-duplicates=MAPPING_FILE
-
--strict-attributes
-
--version
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-f FEATURE_TYPE, --feature=FEATURE_TYPE
-
-h, --help
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-i ID_ATTRIBUTE, --id-attribute=ID_ATTRIBUTE
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-o OUT_FILE
-
-o OUTFILE
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-o OUTPUT_GFF
-
-t FEATURE_TYPE, --type=FEATURE_TYPE
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