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 <[email protected]> Thu, 23 Apr 2020 13:48:28 +0200 + -- Steffen Moeller <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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