From 33c826bb5c78e0a9f0620d076c17e9d122e74f7f Mon Sep 17 00:00:00 2001 From: shinthor <44301097+shinthor@users.noreply.github.com> Date: Fri, 29 Sep 2023 11:41:35 -0400 Subject: [PATCH 1/3] Remove the hardcoded trim tail and trim front length limitations Update options.cpp --- src/options.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/options.cpp b/src/options.cpp index fe9a20b..3f11e05 100644 --- a/src/options.cpp +++ b/src/options.cpp @@ -283,16 +283,16 @@ bool Options::validate() { thread = 16; } - if(trim.front1 < 0 || trim.front1 > 30) + if(trim.front1 < 0) error_exit("trim_front1 (--trim_front1) should be 0 ~ 30, suggest 0 ~ 4"); - if(trim.tail1 < 0 || trim.tail1 > 100) + if(trim.tail1 < 0) error_exit("trim_tail1 (--trim_tail1) should be 0 ~ 100, suggest 0 ~ 4"); - if(trim.front2 < 0 || trim.front2 > 30) + if(trim.front2 < 0) error_exit("trim_front2 (--trim_front2) should be 0 ~ 30, suggest 0 ~ 4"); - if(trim.tail2 < 0 || trim.tail2 > 100) + if(trim.tail2 < 0) error_exit("trim_tail2 (--trim_tail2) should be 0 ~ 100, suggest 0 ~ 4"); if(qualfilter.qualifiedQual - 33 < 0 || qualfilter.qualifiedQual - 33 > 93) From f81ccc393c54dbf9a89087f4167e4bd5f796b0df Mon Sep 17 00:00:00 2001 From: shinthor <44301097+shinthor@users.noreply.github.com> Date: Sat, 7 Oct 2023 15:18:25 -0400 Subject: [PATCH 2/3] switch conda badge to link to my forked conda link --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index bee7909..9409ef5 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ [![install with conda]( -https://anaconda.org/bioconda/fastp/badges/version.svg)](https://anaconda.org/bioconda/fastp) +https://anaconda.org/bioconda/fastp/badges/version.svg)](https://anaconda.org/shinthor/fastp) [![install with conda]( -https://anaconda.org/bioconda/fastp/badges/downloads.svg)](https://anaconda.org/bioconda/fastp) +https://anaconda.org/bioconda/fastp/badges/downloads.svg)](https://anaconda.org/shinthor/fastp) [![DebianBadge]( https://badges.debian.net/badges/debian/unstable/fastp/version.svg)](https://packages.debian.org/unstable/fastp) [![fastp ci](https://github.com/OpenGene/fastp/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/OpenGene/fastp/actions/workflows/ci.yml) From 71fc39fc59036a7a49cfad048b4729d2417c5fda Mon Sep 17 00:00:00 2001 From: shinthor <44301097+shinthor@users.noreply.github.com> Date: Sat, 7 Oct 2023 15:19:08 -0400 Subject: [PATCH 3/3] fix badge image for conda --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9409ef5..e8ca62f 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ [![install with conda]( -https://anaconda.org/bioconda/fastp/badges/version.svg)](https://anaconda.org/shinthor/fastp) +https://anaconda.org/shinthor/fastp/badges/version.svg)](https://anaconda.org/shinthor/fastp) [![install with conda]( -https://anaconda.org/bioconda/fastp/badges/downloads.svg)](https://anaconda.org/shinthor/fastp) +https://anaconda.org/shinthor/fastp/badges/downloads.svg)](https://anaconda.org/shinthor/fastp) [![DebianBadge]( https://badges.debian.net/badges/debian/unstable/fastp/version.svg)](https://packages.debian.org/unstable/fastp) [![fastp ci](https://github.com/OpenGene/fastp/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/OpenGene/fastp/actions/workflows/ci.yml)