Commit 40287997 authored by Ruqian Lyu's avatar Ruqian Lyu
Browse files

fix default value not passed for cmPmb

parent 1c69f700
Pipeline #6981 passed with stages
in 2 minutes and 18 seconds
......@@ -173,7 +173,7 @@ Arguments:
Options:
-t --threads <threads> number of BAM decompression threads [default: 4]
-cb --cellbarcode <cellbarcode> the cell barcode tag, by default it is CB
-cb --cellbarcode <cellbarcode> the cell barcode tag, by default it is CB [default: 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)
......@@ -184,7 +184,7 @@ Options:
-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]
-cmPmb --cmPmb <cmPmb> the average centiMorgan distances per megabases default 0.1 cm per Mb [default: 0.1]
-h --help show help
Examples
......@@ -211,7 +211,7 @@ Options:
cmPmb:float
barcodeTag="CB"
threads = parse_int($args["--threads"])
barcodeTag = $args["--barcodeTag"]
barcodeTag = $args["--cellbarcode"]
mindp = parse_int($args["--minDP"])
maxdp = parse_int($args["--maxDP"])
maxtotal = parse_int($args["--maxTotalDP"])
......
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