[med-svn] [Git][med-team/nanopolish][master] 4 commits: routine-update: New upstream version

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / nanopolish


Commits:
33ce6e28 by Steffen Moeller at 2020-05-03T19:25:11+02:00
routine-update: New upstream version

- - - - -
55e72c8d by Steffen Moeller at 2020-05-03T19:25:12+02:00
New upstream version 0.13.2
- - - - -
96392884 by Steffen Moeller at 2020-05-03T19:25:24+02:00
Update upstream source from tag 'upstream/0.13.2'

Update to upstream version '0.13.2'
with Debian dir 482bb7919af06178c32028d08ea7bef5d9edaff4
- - - - -
6fa303ab by Steffen Moeller at 2020-05-03T19:28:45+02:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- README.md
- debian/changelog
- debian/control
- 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)


=====================================
debian/changelog
=====================================
@@ -1,10 +1,11 @@
-nanopolish (0.13.1-1) UNRELEASED; urgency=medium
+nanopolish (0.13.2-1) unstable; urgency=medium
 
+  [ Michael R. Crusoe ]
   * Team upload.
   * New upstream version
   * Enable building anywhere, there are no longer any SIMD intrinsics
 
- -- Michael R. Crusoe <michael.crusoe at gmail.com>  Thu, 23 Apr 2020 13:48:28 +0200
+ -- Steffen Moeller <moeller at debian.org>  Sun, 03 May 2020 19:25:27 +0200
 
 nanopolish (0.12.1-2) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 12),
                libfast5-dev (>= 0.6.5),
                libhts-dev,
                libeigen3-dev,
-               libminimap2-dev (>= 2.17+dfsg-8)
+               libminimap2-dev
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/nanopolish
 Vcs-Git: https://salsa.debian.org/med-team/nanopolish.git


=====================================
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/-/compare/61a7441722fc79f59acf8db2ad0b19ee45f2a40a...6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7

-- 
View it on GitLab: https://salsa.debian.org/med-team/nanopolish/-/compare/61a7441722fc79f59acf8db2ad0b19ee45f2a40a...6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7
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