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fix partition-before-pggb -p bug
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subwaystation committed Aug 22, 2023
1 parent 936a2c6 commit f50fa66
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion partition-before-pggb
Original file line number Diff line number Diff line change
Expand Up @@ -573,7 +573,7 @@ ls "$prefix_paf".community.*.$fasta_ext | while read community; do
cat <<EOT | tee -a "$log_file" "$param_file"
pggb -i $community \\
-o $community.out \\
-p $segment_length -l $block_length -p $map_pct_id -n $n_mappings -K $mash_kmer -F $mash_kmer_thres \\
-s $segment_length -l $block_length -p $map_pct_id -n $n_mappings -K $mash_kmer -F $mash_kmer_thres \\
-k $min_match_length -f $sparse_factor -B $transclose_batch \\
-H $n_haps -j $max_path_jump -e $max_edge_jump -G $target_poa_length $poa_params_cmd -O $poa_padding -d $pad_max_depth -Q $consensus_prefix \\
$params
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