From 70301f15a2f647813067d2ff56ed6924f5532668 Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Mon, 4 Mar 2024 12:05:44 -0500 Subject: [PATCH] add some newlines --- read_utils.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/read_utils.py b/read_utils.py index a276a907..272d7b3b 100755 --- a/read_utils.py +++ b/read_utils.py @@ -1309,6 +1309,7 @@ def parser_align_and_fix(parser=argparse.ArgumentParser()): dest="novoalign_license_path", help='A path to the novoalign.lic file. This overrides the NOVOALIGN_LICENSE_PATH environment variable. (default: %(default)s)' ) + util.cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None))) util.cmd.attach_main(parser, align_and_fix, split_args=True) return parser @@ -1353,6 +1354,7 @@ def parser_filter_bam_to_proper_primary_mapped_reads(parser=argparse.ArgumentPar help='Reject reads that are not properly paired (default: %(default)s)', action='store_true' ) + util.cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None))) util.cmd.attach_main(parser, filter_bam_to_proper_primary_mapped_reads, split_args=True) return parser @@ -1416,6 +1418,7 @@ def parser_minimap2_idxstats(parser=argparse.ArgumentParser()): ) parser.add_argument('--outBam', help='Output aligned, indexed BAM file', default=None) parser.add_argument('--outStats', help='Output idxstats file', default=None) + util.cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None))) util.cmd.attach_main(parser, minimap2_idxstats, split_args=True) return parser @@ -1504,6 +1507,7 @@ def parser_bwamem_idxstats(parser=argparse.ArgumentParser()): help='Reject reads that are not properly paired (default: %(default)s)', action='store_true' ) + util.cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None))) util.cmd.attach_main(parser, bwamem_idxstats, split_args=True) return parser