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Fixed the help string for poly-a detection.
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kdolan1973 committed Dec 4, 2023
1 parent cb9a82f commit f30cece
Showing 1 changed file with 4 additions and 1 deletion.
5 changes: 4 additions & 1 deletion dorado/cli/basecaller.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -420,7 +420,7 @@ int basecaller(int argc, char* argv[]) {
parser.visible.add_argument("--estimate-poly-a")
.help("Estimate poly-A/T tail lengths (beta feature). Primarily meant for cDNA and "
"dRNA use cases. Note that if this flag is set, then adapter/primer detection "
"be disabled.")
"will be disabled.")
.default_value(false)
.implicit_value(true);

Expand Down Expand Up @@ -528,6 +528,9 @@ int basecaller(int argc, char* argv[]) {
std::exit(EXIT_FAILURE);
}
no_trim_primers = no_trim_adapters = true;
spdlog::info(
"Estimation of poly-a has been requested, so adapter/primer trimming has been "
"disabled.");
}

if (parser.visible.is_used("--kit-name") && parser.visible.is_used("--barcode-arrangement")) {
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