Commit 62b0e420 authored by Ruqian Lyu's avatar Ruqian Lyu
Browse files

change help message to ensure correct args parsing

parent da3375f9
Pipeline #7319 passed with stages
in 1 minute and 4 seconds
......@@ -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
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