[med-svn] [Git][med-team/fastp][master] 3 commits: routine-update: New upstream version

[Dylan Aïssi (@daissi)]

Dylan Aïssi pushed to branch master at Debian Med / fastp


Commits:
8c98097a by Dylan Aïssi at 2021-12-07T22:34:19+01:00
routine-update: New upstream version

- - - - -
7e199d9e by Dylan Aïssi at 2021-12-07T22:34:20+01:00
New upstream version 0.23.2+dfsg
- - - - -
f4413b38 by Dylan Aïssi at 2021-12-07T22:34:20+01:00
Update upstream source from tag 'upstream/0.23.2+dfsg'

Update to upstream version '0.23.2+dfsg'
with Debian dir 4729092fd9484fb504503ed0380a1e22785511fb
- - - - -


4 changed files:

- debian/changelog
- src/common.h
- src/peprocessor.cpp
- src/read.cpp


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+fastp (0.23.2+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+
+ -- Dylan Aïssi <daissi at debian.org>  Tue, 07 Dec 2021 22:34:19 +0100
+
 fastp (0.23.1+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=====================================
src/common.h
=====================================
@@ -1,7 +1,7 @@
 #ifndef COMMON_H
 #define COMMON_H
 
-#define FASTP_VER "0.23.1"
+#define FASTP_VER "0.23.2"
 
 #define _DEBUG false
 


=====================================
src/peprocessor.cpp
=====================================
@@ -923,8 +923,8 @@ void PairEndProcessor::interleavedReaderTask()
             mRightPackReadCounter++;
 
             //re-initialize data for next pack
-            Read** dataLeft = new Read*[PACK_SIZE];
-            Read** dataRight = new Read*[PACK_SIZE];
+            dataLeft = new Read*[PACK_SIZE];
+            dataRight = new Read*[PACK_SIZE];
             memset(dataLeft, 0, sizeof(Read*)*PACK_SIZE);
             memset(dataRight, 0, sizeof(Read*)*PACK_SIZE);
             // if the consumer is far behind this producer, sleep and wait to limit memory usage
@@ -961,10 +961,17 @@ void PairEndProcessor::interleavedReaderTask()
         }
     }
 
+    for(int t=0; t<mOptions->thread; t++) {
+        mLeftInputLists[t]->setProducerFinished();
+        mRightInputLists[t]->setProducerFinished();
+    }
+
+    if(mOptions->verbose) {
+        loginfo("interleaved: loading completed with " + to_string(mLeftPackReadCounter) + " packs");
+    }
+
     mLeftReaderFinished = true;
     mRightReaderFinished = true;
-    if(mOptions->verbose)
-        loginfo("Reads loading: completed");
 
     // if the last data initialized is not used, free it
     if(dataLeft != NULL)


=====================================
src/read.cpp
=====================================
@@ -1,5 +1,6 @@
 #include "read.h"
 #include <sstream>
+#include <cstring>
 #include "util.h"
 
 Read::Read(string* name, string* seq, string* strand, string* quality, bool phred64){



View it on GitLab: https://salsa.debian.org/med-team/fastp/-/compare/f97ad446e7f1e9b6baf09d0d5acdea75ebd728fa...f4413b380fb5c58b195dd34e6874dee186044c41

-- 
View it on GitLab: https://salsa.debian.org/med-team/fastp/-/compare/f97ad446e7f1e9b6baf09d0d5acdea75ebd728fa...f4413b380fb5c58b195dd34e6874dee186044c41
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