replace >=qual by >qual in typo

HKU-BAL · Oct 19, 2021 · 687305d · 687305d
1 parent 4ef9711
commit 687305d
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -342,7 +342,7 @@ docker run -it hkubal/clair3:latest /opt/bin/run_clair3.sh --help
       --vcf_fn=FILE             Candidate sites VCF file input, variants will only be called at the sites in the VCF file if provided.
       --ctg_name=STR            The name of the sequence to be processed.
       --sample_name=STR         Define the sample name to be shown in the VCF file.
-      --qual=INT                If set, variants with >=$qual will be marked PASS, or LowQual otherwise.
+      --qual=INT                If set, variants with >$qual will be marked PASS, or LowQual otherwise.
       --samtools=STR            Path of samtools, samtools version >= 1.10 is required.
       --python=STR              Path of python, python3 >= 3.6 is required.
       --pypy=STR                Path of pypy3, pypy3 >= 3.6 is required.

diff --git a/preprocess/MergeVcf.py b/preprocess/MergeVcf.py
@@ -314,7 +314,7 @@ def main():
                         help="Process variant only in the provided regions prefix")
 
     parser.add_argument('--qual', type=int, default=2,
-                        help="If set, variants with >=$qual will be marked 'PASS', or 'LowQual' otherwise, optional")
+                        help="If set, variants with >$qual will be marked 'PASS', or 'LowQual' otherwise, optional")
 
     parser.add_argument('--sampleName', type=str, default="SAMPLE",
                         help="Define the sample name to be shown in the VCF file")

diff --git a/run_clair3.sh b/run_clair3.sh
@@ -25,7 +25,7 @@ print_help_messages()
     echo $'      --vcf_fn=FILE             Candidate sites VCF file input, variants will only be called at the sites in the VCF file if provided.'
     echo $'      --ctg_name=STR            The name of the sequence to be processed.'
     echo $'      --sample_name=STR         Define the sample name to be shown in the VCF file.'
-    echo $'      --qual=INT                If set, variants with >=$qual will be marked PASS, or LowQual otherwise.'
+    echo $'      --qual=INT                If set, variants with >$qual will be marked PASS, or LowQual otherwise.'
     echo $'      --samtools=STR            Path of samtools, samtools version >= 1.10 is required.'
     echo $'      --python=STR              Path of python, python3 >= 3.6 is required.'
     echo $'      --pypy=STR                Path of pypy3, pypy3 >= 3.6 is required.'