From f195246b421a8a4b0cfa3f8bd9fde7a7be366fd6 Mon Sep 17 00:00:00 2001 From: Ivan Blagoev Topolsky Date: Wed, 21 Sep 2022 17:17:38 +0200 Subject: [PATCH] A bit more explicit about array base --- scripts/aln2basecnt | 2 +- scripts/extract_coverage_intervals | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/aln2basecnt b/scripts/aln2basecnt index ad0f5f7..baa7565 100755 --- a/scripts/aln2basecnt +++ b/scripts/aln2basecnt @@ -48,7 +48,7 @@ def parse_args(): type=str, dest='alpha', help='alphabet to use') parser.add_argument('-f', '--first', metavar='ARRAY_BASE', required=False, default=0, choices=[0,1], - type=int, dest='first', help='select whether the first position is named "0" (standard for python tools such as pysam and older versions of smallgenomeutilities) or "1" (standard scientific notation used in most tools)') + type=int, dest='first', help='select whether the first position is named "0" (standard for python tools such as pysam, older versions of smallgenomeutilities, and the BED format) or "1" (standard scientific notation used in most tools, and most text formats such as VCF and GFF)') parser.add_argument('-s', '--stats', metavar='YAML/JSON/INI', required=False, type=str, dest='stats', help="file to write stats to") parser.add_argument("FILE", nargs=1, metavar='BAM/CRAM', help="alignment file") diff --git a/scripts/extract_coverage_intervals b/scripts/extract_coverage_intervals index b872c0a..2ede8bb 100755 --- a/scripts/extract_coverage_intervals +++ b/scripts/extract_coverage_intervals @@ -36,7 +36,7 @@ def parse_args(): ) parser.add_argument( "-b", "--based", "--first", required=False, default=0, choices=[0, 1], type=int, metavar='INPUTBASED', dest='based', - help="Specifies whether the input TSV is 0-based (as used by python tools such as pysam) or 1-based (as standard notation in genetics), and thus should be converted before outputing the 0-based output." + help="Specifies whether the input TSV is 0-based (as used by python tools such as pysamm, or in BED files) or 1-based (as standard notation in genetics, or in VCF files), and thus should be converted before outputing the 0-based output." "are interpreted using 0-based indexing, and a half-open " "interval is used, i.e, [start:end)" )