[med-svn] [Git][med-team/fastp][upstream] New upstream version 0.23.2+dfsg

[Dylan Aïssi (@daissi)]

Dylan Aïssi pushed to branch upstream at Debian Med / fastp


Commits:
7e199d9e by Dylan Aïssi at 2021-12-07T22:34:20+01:00
New upstream version 0.23.2+dfsg
- - - - -


3 changed files:

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


Changes:

=====================================
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/-/commit/7e199d9ed5dd4ba5a46ce6ed0937dba0d261a862

-- 
View it on GitLab: https://salsa.debian.org/med-team/fastp/-/commit/7e199d9ed5dd4ba5a46ce6ed0937dba0d261a862
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