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BioCellGen-public
sscocaller
Commits
40287997
Commit
40287997
authored
Jun 23, 2021
by
Ruqian Lyu
Browse files
fix default value not passed for cmPmb
parent
1c69f700
Pipeline
#6981
passed with stages
in 2 minutes and 18 seconds
Changes
1
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1
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src/sscocaller.nim
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40287997
...
...
@@ -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
[
"--barcode
Tag
"
]
barcodeTag
=
$
args
[
"--
cell
barcode"
]
mindp
=
parse_int
(
$
args
[
"--minDP"
]
)
maxdp
=
parse_int
(
$
args
[
"--maxDP"
]
)
maxtotal
=
parse_int
(
$
args
[
"--maxTotalDP"
]
)
...
...
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