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Fixes in partition-before-pggb #349

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Nov 2, 2023
Merged

Fixes in partition-before-pggb #349

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4 changes: 2 additions & 2 deletions partition-before-pggb
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Original file line number Diff line number Diff line change
Expand Up @@ -545,7 +545,7 @@ if [[ $sparse_map != false ]]; then
params="$params -x $sparse_map"
fi
if [[ $exclude_delim != false ]]; then
params="$params -Y $exclude_delim"
params="$params -Y \"$exclude_delim\""
fi
if [[ $skip_normalization != false ]]; then
params="$params --skip-normalization"
Expand Down Expand Up @@ -608,7 +608,7 @@ pggb -i $community \\
-o $community.out \\
-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 \\
-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
EOT
done
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