From 638f2ce8b9c266d07791baadcf47a29c1a85b7d0 Mon Sep 17 00:00:00 2001 From: Shifu Chen Date: Mon, 6 Aug 2018 08:04:09 +0800 Subject: [PATCH] Update README.md --- README.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 1107060..ac6fe6d 100644 --- a/README.md +++ b/README.md @@ -90,7 +90,17 @@ pxz -9 in.rfq Tips: * lower compression ratio than `-9` is not recommended, since it will not be faster. The difference is the RAM requirement. -``` + +# STDIN and STDOUT +repaq can read the input from STDIN, and write the output to STDOUT. +* specify `--stdin` if you want to read the STDIN for compression or decompression. +* specify `--stdout` if you want to output to the STDOUT for compression or decompression. +* in decompression mode, if `--stdout` is specified, the output will be interleaved PE stream. +* if the STDIN is an interleaved paired-end stream, specify `--interleaved_in` to indicate that. + +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 ``` # FASTQ Format compatibility