From 402879977033bc8bd09d115480565fca28a952dd Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Wed, 23 Jun 2021 10:58:36 +1000
Subject: [PATCH] fix default value not passed for cmPmb
---
src/sscocaller.nim | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/sscocaller.nim b/src/sscocaller.nim
index 6f2fb95..3ee6077 100755
--- a/src/sscocaller.nim
+++ b/src/sscocaller.nim
@@ -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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