Dylan Aïssi pushed to branch master at Debian Med / fastp
Commits: 2c6af5bd by Dylan Aïssi at 2021-11-19T16:29:47+01:00 New upstream version 0.23.1+dfsg - - - - - c8ac5dfa by Dylan Aïssi at 2021-11-19T16:29:47+01:00 routine-update: New upstream version - - - - - 0f315940 by Dylan Aïssi at 2021-11-19T16:29:47+01:00 Update upstream source from tag 'upstream/0.23.1+dfsg' Update to upstream version '0.23.1+dfsg' with Debian dir 08196720c28eb569a66f80fea788330c73516701 - - - - - cd303ebf by Dylan Aïssi at 2021-11-19T16:29:53+01:00 Set upstream metadata fields: Repository, Repository-Browse. - - - - - f97ad446 by Dylan Aïssi at 2021-11-19T16:30:48+01:00 routine-update: Ready to upload to unstable - - - - - 5 changed files: - README.md - debian/changelog - debian/upstream/metadata - src/common.h - src/peprocessor.cpp Changes: ===================================== README.md ===================================== @@ -64,7 +64,8 @@ A tool designed to provide fast all-in-one preprocessing for FastQ files. This t 11. support long reads (data from PacBio / Nanopore devices). 12. support reading from STDIN and writing to STDOUT 13. support interleaved input -14. ... +14. support ultra-fast FASTQ-level deduplication +15. ... This tool is being intensively developed, and new features can be implemented soon if they are considered useful. If you have any additional requirement for `fastp`, please file an issue:https://github.com/OpenGene/fastp/issues/new @@ -93,15 +94,15 @@ https://anaconda.org/bioconda/fastp/badges/version.svg)](https://anaconda.org/bi conda install -c bioconda fastp ``` ## or download the latest prebuilt binary for Linux users -Tthis binary was compiled on CentOS, and tested on CentOS/Ubuntu +This binary was compiled on CentOS, and tested on CentOS/Ubuntu ```shell # download the latest build wget http://opengene.org/fastp/fastp chmod a+x ./fastp -# or download specified version, i.e. fastp v0.20.1 -wget http://opengene.org/fastp/fastp.0.20.1 -mv fastp.0.20.1 fastp +# or download specified version, i.e. fastp v0.23.1 +wget http://opengene.org/fastp/fastp.0.23.1 +mv fastp.0.23.1 fastp chmod a+x ./fastp ``` ## or compile from source ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +fastp (0.23.1+dfsg-1) unstable; urgency=medium + + * New upstream version + * Set upstream metadata fields: Repository, Repository-Browse. + + -- Dylan Aïssi <[email protected]> Fri, 19 Nov 2021 16:29:53 +0100 + fastp (0.23.0+dfsg-1) unstable; urgency=medium * Team upload. ===================================== debian/upstream/metadata ===================================== @@ -19,3 +19,5 @@ Registry: Entry: NA - Name: conda:bioconda Entry: fastp +Repository: https://github.com/OpenGene/fastp.git +Repository-Browse: https://github.com/OpenGene/fastp ===================================== src/common.h ===================================== @@ -1,7 +1,7 @@ #ifndef COMMON_H #define COMMON_H -#define FASTP_VER "0.23.0" +#define FASTP_VER "0.23.1" #define _DEBUG false ===================================== src/peprocessor.cpp ===================================== @@ -109,11 +109,11 @@ void PairEndProcessor::closeOutput() { } if(mUnpairedLeftWriter) { delete mUnpairedLeftWriter; - mLeftWriter = NULL; + mUnpairedLeftWriter = NULL; } if(mUnpairedRightWriter) { delete mUnpairedRightWriter; - mRightWriter = NULL; + mUnpairedRightWriter = NULL; } } @@ -555,11 +555,15 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T } } } else if( r2 != NULL && result2 == PASS_FILTER) { - if(mUnpairedLeftWriter || mUnpairedRightWriter) { + if(mUnpairedRightWriter) { r2->appendToString(unpairedOut2); if(mFailedWriter) or1->appendToStringWithTag(failedOut,FAILED_TYPES[result1]); - } else { + } else if(mUnpairedLeftWriter) { + r2->appendToString(unpairedOut1); + if(mFailedWriter) + or1->appendToStringWithTag(failedOut,FAILED_TYPES[result1]); + } else { if(mFailedWriter) { or1->appendToStringWithTag(failedOut, FAILED_TYPES[result1]); or2->appendToStringWithTag(failedOut, "paired_read_is_failing"); @@ -648,9 +652,6 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T } else if(mUnpairedLeftWriter) { mUnpairedLeftWriter->input(tid, unpairedOut1); unpairedOut1 = NULL; - - mUnpairedLeftWriter->input(tid, unpairedOut2); - unpairedOut2 = NULL; } if(mOptions->split.byFileLines) View it on GitLab: https://salsa.debian.org/med-team/fastp/-/compare/85a7aa3e316d38c2ea0a9caf44495c972f74de45...f97ad446e7f1e9b6baf09d0d5acdea75ebd728fa -- View it on GitLab: https://salsa.debian.org/med-team/fastp/-/compare/85a7aa3e316d38c2ea0a9caf44495c972f74de45...f97ad446e7f1e9b6baf09d0d5acdea75ebd728fa You're receiving this email because of your account on salsa.debian.org.
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