From 62b0e42065670d5b1dadaf33d0c67fcaadd58900 Mon Sep 17 00:00:00 2001 From: rlyu <rlyu@svi.edu.au> Date: Tue, 20 Jul 2021 13:13:24 +1000 Subject: [PATCH] change help message to ensure correct args parsing --- src/sscocaller.nim | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/sscocaller.nim b/src/sscocaller.nim index 4624cd6..ce0cda6 100755 --- a/src/sscocaller.nim +++ b/src/sscocaller.nim @@ -426,17 +426,17 @@ Arguments: Options: -t --threads <threads> number of BAM decompression threads [default: 4] -cb --cellbarcode <cellbarcode> the cell barcode tag, by default it is CB - -MQ --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20] - -BQ --baseq <baseq> base quality threshold for a base to be used for counting [default: 13] - -CHR --chrom <chrom> the selected chromsome (whole genome if not supplied,separate by comma if multiple chroms) - -minDP --minDP <minDP> the minimum DP for a SNP to be included in the output file [default: 1] - -maxDP --maxDP <maxDP> the maximum DP for a SNP to be included in the output file [default: 5] - -maxTotalDP --maxTotalDP <maxTotalDP> the maximum DP across all barcodes for a SNP to be included in the output file [default: 25] - -minTotalDP --minTotalDP <minTotalDP> the minimum DP across all barcodes for a SNP to be included in the output file [default: 10] - -chrName --chrName <chrName> the chr names with chr prefix or not, if not supplied then no prefix - -thetaREF --thetaREF <thetaREF> the theta for the binomial distribution conditioning on hidden state being REF [default: 0.1] - -thetaALT --thetaALT <thetaALT> the theta for the binomial distribution conditioning on hidden state being ALT [default: 0.9] - -cmPmb --cmPmb <cmPmb> the average centiMorgan distances per megabases default 0.1 cm per Mb [default 0.1] + --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20] + --baseq <baseq> base quality threshold for a base to be used for counting [default: 13] + --chrom <chrom> the selected chromsome (whole genome if not supplied,separate by comma if multiple chroms) + --minDP <minDP> the minimum DP for a SNP to be included in the output file [default: 1] + --maxDP <maxDP> the maximum DP for a SNP to be included in the output file [default: 5] + --maxTotalDP <maxTotalDP> the maximum DP across all barcodes for a SNP to be included in the output file [default: 25] + --minTotalDP <minTotalDP> the minimum DP across all barcodes for a SNP to be included in the output file [default: 10] + --chrName <chrName> the chr names with chr prefix or not, if not supplied then no prefix + --thetaREF <thetaREF> the theta for the binomial distribution conditioning on hidden state being REF [default: 0.1] + --thetaALT <thetaALT> the theta for the binomial distribution conditioning on hidden state being ALT [default: 0.9] + --cmPmb <cmPmb> the average centiMorgan distances per megabases default 0.1 cm per Mb [default 0.1] -h --help show help Examples -- GitLab