I’ve been using NucDiff successfully, but would like to override defaults via the --nucmer_opt option, specifically I’d like to invoke –-nooptimize rather than the default –-optimize.
I’ve tried including –-nucmer_opt ‘--nooptimize’
and --nucmer_opt ‘nooptimize’
…and other attempts,
but they all result in error, for example:
nucdiff --vcf yes --ref_name_full yes --query_name_full yes --nucmer_opt '--nooptimize' nc_045512_wg.fasta VIRAL_FASTA/227-M50450.fasta NUCDIFF_OUT_T153G_nooptimize 227-M50450.fasta
usage: nucdiff [-h] [--reloc_dist [int]] [--nucmer_opt [NUCMER_OPT]]
[--filter_opt [FILTER_OPT]] [--delta_file [DELTA_FILE]]
[--proc [int]] [--ref_name_full [{yes,no}]]
[--query_name_full [{yes,no}]] [--vcf [{yes,no}]] [--version]
Reference.fasta Query.fasta Output_dir Prefix
nucdiff: error: unrecognized arguments: --nooptimize
I appreciate your time, if you (or co-authors) have any suggestions, that would be great. Thanks.
—Mike
I’ve been using NucDiff successfully, but would like to override defaults via the --nucmer_opt option, specifically I’d like to invoke –-nooptimize rather than the default –-optimize.
I’ve tried including –-nucmer_opt ‘--nooptimize’
and --nucmer_opt ‘nooptimize’
…and other attempts,
but they all result in error, for example:
nucdiff --vcf yes --ref_name_full yes --query_name_full yes --nucmer_opt '--nooptimize' nc_045512_wg.fasta VIRAL_FASTA/227-M50450.fasta NUCDIFF_OUT_T153G_nooptimize 227-M50450.fasta
usage: nucdiff [-h] [--reloc_dist [int]] [--nucmer_opt [NUCMER_OPT]]
[--filter_opt [FILTER_OPT]] [--delta_file [DELTA_FILE]]
[--proc [int]] [--ref_name_full [{yes,no}]]
[--query_name_full [{yes,no}]] [--vcf [{yes,no}]] [--version]
Reference.fasta Query.fasta Output_dir Prefix
nucdiff: error: unrecognized arguments: --nooptimize
I appreciate your time, if you (or co-authors) have any suggestions, that would be great. Thanks.
—Mike