From 6ffb32ddb02bc83281859f01ff09026ede9c3ac2 Mon Sep 17 00:00:00 2001 From: Shifu Chen Date: Mon, 6 Aug 2018 08:05:18 +0800 Subject: [PATCH] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ac6fe6d..e40c7c6 100644 --- a/README.md +++ b/README.md @@ -100,7 +100,7 @@ repaq can read the input from STDIN, and write the output to STDOUT. Here gives you an example of compressing the interleaved PE output from fastp by directly using pipes: ```shell -fastp -i R1.fq -I R2.fq --stdout | repaq --interleaved_in --stdin --stdout | xz > out.rpq.xz +fastp -i R1.fq -I R2.fq --stdout | repaq -c --interleaved_in --stdin --stdout | xz > out.rpq.xz ``` # FASTQ Format compatibility @@ -119,7 +119,7 @@ options: -o, --out1 output file name (string [=]) -I, --in2 read2 input file name when encoding paired-end FASTQ files (string [=]) -O, --out2 read2 output file name when decoding to paired-end FASTQ files (string [=]) - -c, --compress compress input to output + -c, --compress compress input to output. This is the default mode -d, --decompress decompress input to output -k, --chunk the chunk size (kilo bases) for encoding, default 1000=1000kb. (int [=1000]) --stdin input from STDIN. If the STDIN is interleaved paired-end FASTQ, please also add --interleaved_in.