From 3a7fb7c5b9f04cd879bb354377f96bd74f6e4c02 Mon Sep 17 00:00:00 2001 From: fangli80 Date: Fri, 24 Jun 2022 02:24:59 +0800 Subject: [PATCH] change alignment parameters --- nanoRepeat_bam.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nanoRepeat_bam.py b/nanoRepeat_bam.py index af7e016..d99066c 100644 --- a/nanoRepeat_bam.py +++ b/nanoRepeat_bam.py @@ -356,7 +356,7 @@ def round1_and_round2_estimation(minimap2: string, repeat_region: RepeatRegion, round1_paf_file = os.path.join(repeat_region.temp_out_dir, 'round1.paf') repeat_region.temp_file_list.append(round1_paf_file) - minimap2_parameters = ' -x map-ont -B 9 ' + minimap2_parameters = ' -x map-ont ' cmd = f'{minimap2} -c -t {num_cpu} {minimap2_parameters} {round1_fasta_file} {repeat_region.core_seq_fq_file} > {round1_paf_file} 2> /dev/null' tk.eprint(f'NOTICE: running command: {cmd}') @@ -835,7 +835,7 @@ def round3_estimation(minimap2:string, repeat_region:RepeatRegion, num_cpu:int): round3_paf_file = os.path.join(repeat_region.temp_out_dir, 'round3.paf') repeat_region.temp_file_list.append(round3_paf_file) - minimap2_parameters = ' -x map-ont -B 9 ' + minimap2_parameters = ' -x map-ont ' cmd = f'{minimap2} {minimap2_parameters} -N 100 -c --eqx -t {num_cpu} {template_fasta_file} {repeat_region.core_seq_fq_file} > {round3_paf_file} 2> /dev/null' tk.run_system_cmd(cmd)