From c87069ce2ebb55fc23a2257836940944206d9e37 Mon Sep 17 00:00:00 2001 From: eric Date: Mon, 8 Apr 2024 14:01:02 +0800 Subject: [PATCH] =?UTF-8?q?=E4=BC=98=E5=8C=96=E4=BB=A3=E7=A0=81=E7=BB=93?= =?UTF-8?q?=E6=9E=84?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.md | 6 +++++- kr2r/src/args.rs | 1 + kr2r/src/bin/resolve.rs | 3 ++- 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 07e8ea3..bd94597 100644 --- a/README.md +++ b/README.md @@ -328,7 +328,9 @@ Options: --hash-dir database hash chunk directory and other files --chunk-dir - + chunk directory + --full-output + output file contains all unclassified seq -T, --confidence-threshold Confidence score threshold, default is 0.0 [default: 0] -K, --report-kmer-data @@ -384,6 +386,8 @@ Options: In comb. w/ -R, provide minimizer information in report -z, --report-zero-counts In comb. w/ -R, report taxa w/ 0 count + --full-output + output file contains all unclassified sequence -h, --help Print help (see more with '--help') -V, --version diff --git a/kr2r/src/args.rs b/kr2r/src/args.rs index 257ab7f..e5f5823 100644 --- a/kr2r/src/args.rs +++ b/kr2r/src/args.rs @@ -133,6 +133,7 @@ pub struct ClassifyArgs { #[clap(short = 'z', long, value_parser, default_value_t = false)] pub report_zero_counts: bool, + /// output file contains all unclassified sequence #[clap(long, value_parser, default_value_t = false)] pub full_output: bool, diff --git a/kr2r/src/bin/resolve.rs b/kr2r/src/bin/resolve.rs index 04355be..e71a421 100644 --- a/kr2r/src/bin/resolve.rs +++ b/kr2r/src/bin/resolve.rs @@ -153,10 +153,11 @@ pub struct Args { #[clap(long)] pub hash_dir: PathBuf, - // chunk directory + /// chunk directory #[clap(long, value_parser, required = true)] pub chunk_dir: PathBuf, + /// output file contains all unclassified sequence #[clap(long, value_parser, default_value_t = false)] pub full_output: bool, /// Confidence score threshold, default is 0.0.