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polish: make codon module

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kuoi 2024-12-09 15:34:33 +11:00
parent 4d3b5c2001
commit caf80feabf
1 changed files with 2 additions and 2 deletions
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RGBEPP.d
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@ -19,7 +19,7 @@ void show_help(string pkgver) {
-c\t--config\tconfig file for software path (optional) -c\t--config\tconfig file for software path (optional)
-g\t--genes\t\tgene file path (optional, if -r is specified) -g\t--genes\t\tgene file path (optional, if -r is specified)
-f\t--functions\tfunctions type (optional): all clean map -f\t--functions\tfunctions type (optional): all clean map
\t \tpostmap varcall consen align \t \tpostmap varcall consen codon align trim
-h\t--help\t\tshow this information -h\t--help\t\tshow this information
-l\t--list\t\tlist file path -l\t--list\t\tlist file path
-m\t--memory\tmemory settings (optional, default 16 GB) -m\t--memory\tmemory settings (optional, default 16 GB)
@ -765,7 +765,7 @@ void main(string[] args) {
} }
} }
if (ARG_F == "all" && enableCodon) { if (ARG_F == "all" && enableCodon || ARG_F == "codon") {
if(testFiles([PathExonerate]) && testStringArray(ARG_G) && testString(ARG_R)){ if(testFiles([PathExonerate]) && testStringArray(ARG_G) && testString(ARG_R)){
processCodon(ARG_G, ARG_R, DirConsensus, PathExonerate); //ARG_G processCodon(ARG_G, ARG_R, DirConsensus, PathExonerate); //ARG_G
} else { } else {