diff --git a/partition-before-pggb b/partition-before-pggb index 5b57d39..df1fb8e 100755 --- a/partition-before-pggb +++ b/partition-before-pggb @@ -203,7 +203,7 @@ if [ $show_help == true ]; then echo " -K, --mash-kmer N kmer size for mapping [default: "$MASH_KMER"]" echo " -F, --mash-kmer-thres N ignore the top % most-frequent kmers [default: "$MASH_KMER_THRES"]" echo " -Y, --exclude-delim C skip mappings when the query and target have the same" - echo " prefix before the last occurrence of the given character C [default: #]" + echo " prefix before the last occurrence of the given character C [default: #, assuming PanSN-spec]" echo " [seqwish]" echo " -k, --min-match-len N filter exact matches below this length [default: "$MIN_MATCH_LENGTH"]" echo " -f, --sparse-factor N keep this randomly selected fraction of input matches [default: no sparsification]"