[med-svn] [spades] 01/04: fix spelling

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository spades.

commit b28cec0cdd42710f483bef484de5f15ab2e0e470
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sun Feb 21 23:09:36 2016 +0000

    fix spelling
---
 debian/changelog                   |  6 ++++++
 debian/control                     |  4 +++-
 debian/patches/0112_spelling.patch | 11 +++++++++++
 debian/patches/series              |  2 +-
 4 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 34f0f1a..21490b3 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+spades (3.6.2+dfsg-2) UNRELEASED; urgency=medium
+
+  * Use Debian's jemalloc (Closes: #815374) 
+
+ -- Sascha Steinbiss <sascha at steinbiss.name>  Sun, 21 Feb 2016 11:28:25 +0000
+
 spades (3.6.2+dfsg-1) unstable; urgency=low
 
   * Initial release (Closes: #813988)
diff --git a/debian/control b/debian/control
index 2500a99..8e953b0 100644
--- a/debian/control
+++ b/debian/control
@@ -14,6 +14,7 @@ Build-Depends: debhelper (>= 9),
                libboost-dev,
                libbam-dev,
                libbamtools-dev,
+               libjemalloc-dev,
                libhts-dev,
                python-yaml,
                python-joblib,
@@ -35,7 +36,8 @@ Depends: ${shlibs:Depends},
          python-yaml,
          bwa,
          bamtools,
-         samtools
+         samtools,
+         libjemalloc1
 Description: genome assembler for single-cell and isolates data sets
  The SPAdes – St. Petersburg genome assembler is intended for both
  standard isolates and single-cell MDA bacteria assemblies.  It works
diff --git a/debian/patches/0112_spelling.patch b/debian/patches/0112_spelling.patch
index 553da74..9e4b617 100644
--- a/debian/patches/0112_spelling.patch
+++ b/debian/patches/0112_spelling.patch
@@ -76,3 +76,14 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  			TRACE("New edge1: " << graph_.int_id(split_edges.first) << ", length: " << graph_.length(split_edges.first));
  			TRACE("New edge2: " << graph_.int_id(split_edges.second) << ", length: " << graph_.length(split_edges.second));
  			edge1 = split_edges.first;
+--- a/src/debruijn/simplification.cpp
++++ b/src/debruijn/simplification.cpp
+@@ -91,7 +91,7 @@
+     INFO("Average coverage = " << cfg::get().ds.avg_coverage());
+     if (!cfg::get().ds.single_cell) {
+         if (cfg::get().ds.avg_coverage() < gp.ginfo.ec_bound())
+-            WARN("The determined errorneous connection coverage threshold may be determined improperly\n");
++            WARN("The determined erroneous connection coverage threshold may be determined improperly\n");
+     }
+ }
+ 
diff --git a/debian/patches/series b/debian/patches/series
index d8822cc..61c25b1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -14,4 +14,4 @@
 0111_use_full_config_dirs.patch
 0112_spelling.patch
 0113_adjust_paths.patch
-0120_dont_rename_jemalloc_functionnames.patch
+0114_use_debian_provided_jemalloc.patch

-- 
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