[med-svn] [spades] 03/08: new upstream release

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository spades.

commit 63f26d0de60afd7962055493901020b1793312be
Author: Sascha Steinbiss <satta at debian.org>
Date:   Mon Dec 18 00:24:48 2017 +0000

    new upstream release
---
 debian/changelog                                   |  2 +-
 debian/patches/0003_accept-system-bwa.patch        |  4 ++--
 debian/patches/0114_use_debian_provided_libs.patch | 10 +++++-----
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 818e7b7..520e615 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-spades (3.11.0+dfsg-1) unstable; urgency=medium
+spades (3.11.1+dfsg-1) unstable; urgency=medium
 
   * New upstream release.
 
diff --git a/debian/patches/0003_accept-system-bwa.patch b/debian/patches/0003_accept-system-bwa.patch
index 0fb3707..0b10bac 100644
--- a/debian/patches/0003_accept-system-bwa.patch
+++ b/debian/patches/0003_accept-system-bwa.patch
@@ -79,8 +79,8 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
 +    return None
  
  def fill_cfg(options_to_parse, log, secondary_filling=False):
-     skip_output_dir=secondary_filling
-@@ -502,7 +518,11 @@
+     skip_output_dir = secondary_filling
+@@ -510,7 +526,11 @@
      if (not options_storage.only_error_correction) and options_storage.mismatch_corrector:
          cfg["mismatch_corrector"] = empty_config()
          cfg["mismatch_corrector"].__dict__["skip-masked"] = None
diff --git a/debian/patches/0114_use_debian_provided_libs.patch b/debian/patches/0114_use_debian_provided_libs.patch
index 524b744..f8f6c3b 100644
--- a/debian/patches/0114_use_debian_provided_libs.patch
+++ b/debian/patches/0114_use_debian_provided_libs.patch
@@ -73,16 +73,16 @@ Author: Sascha Steinbiss <satta at debian.org>
  
  #ifdef SPADES_USE_JEMALLOC
 -  const size_t *cmem = 0, *cmem_max = 0;
--  size_t clen = sizeof(cmem);
-+  const size_t *cmem = 0;
-+  size_t clen = sizeof(cmem), *cmem_max = 0;
++  const size_t *cmem = 0;//, *cmem_max = 0;
+   size_t clen = sizeof(cmem);
  
    je_mallctl("stats.cactive", &cmem, &clen, NULL, 0);
 -  je_mallctl("stats.cactive_max", &cmem_max, &clen, NULL, 0);
 +  //je_mallctl("stats.cactive_max", &cmem_max, &clen, NULL, 0);
-+  *cmem_max = utils::get_max_rss();
    mem = (*cmem) / 1024;
-   max_rss = (*cmem_max) / 1024;
+-  max_rss = (*cmem_max) / 1024;
++  //max_rss = (*cmem_max) / 1024;
++  max_rss = utils::get_max_rss();
  #else
 -  max_rss = get_max_rss();
 +  max_rss = utils::get_max_rss();

-- 
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