[med-svn] [Git][med-team/fastp][master] 5 commits: New upstream version 0.23.1+dfsg

[Dylan Aïssi (@daissi)]

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 <daissi at debian.org>  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
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