diff --git a/dorado/cli/trim.cpp b/dorado/cli/trim.cpp index 70cc677b..459fad53 100644 --- a/dorado/cli/trim.cpp +++ b/dorado/cli/trim.cpp @@ -126,12 +126,11 @@ int trim(int argc, char* argv[]) { auto output_mode = OutputMode::BAM; auto emit_fastq = parser.get("--emit-fastq"); - auto emit_sam = !emit_fastq; if (emit_fastq) { spdlog::info(" - Note: FASTQ output is not recommended as not all data can be preserved."); output_mode = OutputMode::FASTQ; - } else if (emit_sam || utils::is_fd_tty(stdout)) { + } else if (utils::is_fd_tty(stdout)) { output_mode = OutputMode::SAM; } else if (utils::is_fd_pipe(stdout)) { output_mode = OutputMode::UBAM;