From f50fa6662cae78ded6cb8557eb90e129d58daf85 Mon Sep 17 00:00:00 2001
From: subwaystation <simon.heumos@qbic.uni-tuebingen.de>
Date: Tue, 22 Aug 2023 11:27:28 +0200
Subject: [PATCH] fix partition-before-pggb -p bug

---
 partition-before-pggb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/partition-before-pggb b/partition-before-pggb
index a1722fa..8ff76af 100755
--- a/partition-before-pggb
+++ b/partition-before-pggb
@@ -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