[med-svn] [Git][med-team/nanopolish][upstream] New upstream version 0.13.2

[Steffen Möller]

Steffen Möller pushed to branch upstream at Debian Med / nanopolish


Commits:
55e72c8d by Steffen Moeller at 2020-05-03T19:25:12+02:00
New upstream version 0.13.2
- - - - -


4 changed files:

- README.md
- src/common/nanopolish_common.h
- src/io/nanopolish_fast5_loader.cpp
- src/nanopolish_squiggle_read.cpp


Changes:

=====================================
README.md
=====================================
@@ -6,6 +6,8 @@ Software package for signal-level analysis of Oxford Nanopore sequencing data. N
 
 ## Release notes
 
+* 0.13.2: fix memory leak when loading signal data
+
 * 0.13.1: fix `nanopolish index` performance issue for some barcoding runs
 
 * 0.13.0: modify HMM transitions to allow the balance between insertions and deletions to be changed depending on mode (consensus vs reference variants)


=====================================
src/common/nanopolish_common.h
=====================================
@@ -18,7 +18,7 @@
 #include "logsum.h"
 
 #define PACKAGE_NAME "nanopolish"
-#define PACKAGE_VERSION "0.13.1"
+#define PACKAGE_VERSION "0.13.2"
 #define PACKAGE_BUGREPORT "https://github.com/jts/nanopolish/issues"
 
 //


=====================================
src/io/nanopolish_fast5_loader.cpp
=====================================
@@ -24,6 +24,9 @@ Fast5Loader::~Fast5Loader()
 Fast5Data Fast5Loader::load_read(const std::string& filename, const std::string& read_name)
 {
     Fast5Data data;
+    data.rt.n = 0;
+    data.rt.raw = NULL;
+
     fast5_file f5_file = fast5_open(filename);
     if(!fast5_is_open(f5_file)) {
         data.is_valid = false;


=====================================
src/nanopolish_squiggle_read.cpp
=====================================
@@ -88,6 +88,8 @@ SquiggleRead::SquiggleRead(const std::string& name, const ReadDB& read_db, const
     if(!this->events[0].empty()) {
         assert(this->base_model[0] != NULL);
     }
+    free(data.rt.raw);
+    data.rt.raw = NULL;
 }
 
 SquiggleRead::SquiggleRead(const ReadDB& read_db, const Fast5Data& data, const uint32_t flags)



View it on GitLab: https://salsa.debian.org/med-team/nanopolish/-/commit/55e72c8dd14f1ea3aaab30db00cf33667602945d

-- 
View it on GitLab: https://salsa.debian.org/med-team/nanopolish/-/commit/55e72c8dd14f1ea3aaab30db00cf33667602945d
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