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Missing documentation of `-ins_length` in oases help message

Open winni2k opened this issue 5 years ago • 0 comments

I am running oases version 0.2.09 installed from bioconda. When I run oases --help, then I get the usage message below, which includes documentation for -ins_length2, but not for -ins_length. This lack of documentation has caused substantial confusion to this user. Perhaps it might be worth including -ins_length in the oases help message.

Usage:
./oases directory [options]

	directory			: working directory name

Standard options:
	--help				: this help message
	--version			: print version and exit
	--citation			: print citation to Oases manuscript and exit
	-ins_length2 <integer>		: expected distance between two paired-end reads in the second short-read dataset (default: no read pairing)
	-ins_length_long <integer>	: expected distance between two long paired-end reads (default: no read pairing)
	-ins_length*_sd <integer>	: est. standard deviation of respective dataset (default: 10% of corresponding length)
		[replace '*' by nothing, '2' or '_long' as necessary]
	-unused_reads <yes|no>		: export unused reads in UnusedReads.fa file (default: no)
	-amos_file <yes|no>		: export assembly to AMOS file (default: no export)
	-alignments <yes|no>		: export a summary of contig alignment to the reference sequences (default: no)

Advanced options:
	-cov_cutoff <floating-point>	: removal of low coverage nodes AFTER tour bus or allow the system to infer it (default: 3)
	-min_pair_count <integer>	: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 4)
	-min_trans_lgth <integer>	: Minimum length of output transcripts (default: hash-length)
	-paired_cutoff <floating-point>	: minimum ratio allowed between the numbers of observed and estimated connecting read pairs
		Must be part of the open interval ]0,1[ (default: 0.1)
	-merge <yes|no>		:Preserve contigs mapping onto long sequences to be preserved from coverage cutoff (default: no)
	-edgeFractionCutoff <floating-point>	: Remove edges which represent less than that fraction of a nodes outgoing flow
		Must be part of the open interval ]0,1[ (default: 0.01)
	-scaffolding <yes|no>		: Allow gaps in transcripts (default: no)
	-degree_cutoff <integer>	: Maximum allowed degree on either end of a contigg to consider it 'unique' (default: 3)

Output:
	directory/transcripts.fa
	directory/contig-ordering.txt

winni2k avatar Mar 09 '19 12:03 winni2k