[med-svn] [adapterremoval] 02/07: New upstream version 2.2.1a

[Andreas Tille]

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tille pushed a commit to branch master
in repository adapterremoval.

commit 39c5a9dcebe20cd7ba20acab56027dac115a453e
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jul 17 12:56:55 2017 +0200

    New upstream version 2.2.1a
---
 .travis.yml  | 12 +++++++++++-
 CHANGES.md   |  6 ++++++
 Makefile     | 10 ++++++++++
 README.md    |  2 +-
 src/fastq.cc |  1 +
 src/main.h   |  2 +-
 6 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index e677399..cbc22b9 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,15 +6,25 @@ compiler:
   - clang
   - gcc
 
+os:
+ - linux
+ - osx
+
 addons:
   apt:
     packages:
       - zlib1g-dev
       - libbz2-dev
 
+before_install:
+  - pip install --user cpp-coveralls
+
 install: true
 
 script:
     - make
-    - make test
+    - make test COVERAGE=yes
     - make validate
+
+after_success:
+  - coveralls --exclude tests --exclude googletest-release-1.8.0 --gcov-options '\-lp'
diff --git a/CHANGES.md b/CHANGES.md
index 445777e..dea14bf 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,9 @@
+
+### Version 2.2.1a - 2017-05-17
+
+  * Fixed compilation on OSX.
+
+
 ### Version 2.2.1 - 2017-05-15
 
   * Numerous spelling errors fixed courtesy of Andreas Tille.
diff --git a/Makefile b/Makefile
index c2015fe..22e9315 100644
--- a/Makefile
+++ b/Makefile
@@ -25,6 +25,8 @@ COLOR_BUILD := yes
 # Debug build; adds warnings and debugging symbols
 DEBUG_BUILD := no
 
+# Include coverage instrumentation in build
+COVERAGE := no
 
 ###############################################################################
 # Makefile internals. Normally you do not need to touch these.
@@ -65,6 +67,14 @@ else
 $(info Building AdapterRemoval with bzip2 support: no)
 endif
 
+ifeq ($(strip ${COVERAGE}), yes)
+$(info Building AdapterRemoval with coverage instrumentation: yes)
+CXXFLAGS := ${CXXFLAGS} --coverage
+DEBUG_BUILD := yes
+else
+$(info Building AdapterRemoval with coverage instrumentation: no)
+endif
+
 ifeq ($(strip ${DEBUG_BUILD}), yes)
 $(info Building AdapterRemoval with debug information: yes)
 CXXFLAGS := ${CXXFLAGS} -g -pedantic -Wall -Wextra -Wcast-align -Wcast-qual \
diff --git a/README.md b/README.md
index 3a71579..63b3c83 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# AdapterRemoval
+# AdapterRemoval [![Travis](https://img.shields.io/travis/MikkelSchubert/adapterremoval/master.svg)](https://travis-ci.org/MikkelSchubert/adapterremoval) [![Coveralls](https://img.shields.io/coveralls/MikkelSchubert/adapterremoval.svg)](https://coveralls.io/github/MikkelSchubert/adapterremoval)
 
 This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is [...]
 
diff --git a/src/fastq.cc b/src/fastq.cc
index 0e5afb3..f2c409c 100644
--- a/src/fastq.cc
+++ b/src/fastq.cc
@@ -24,6 +24,7 @@
 \*************************************************************************/
 #include <algorithm>
 #include <cmath>
+#include <numeric>
 #include <stdexcept>
 #include <sstream>
 
diff --git a/src/main.h b/src/main.h
index 3b8e3af..23c86b1 100644
--- a/src/main.h
+++ b/src/main.h
@@ -31,7 +31,7 @@ namespace ar
 {
 
 const std::string NAME = "AdapterRemoval";
-const std::string VERSION = "ver. 2.2.1";
+const std::string VERSION = "ver. 2.2.1a";
 const std::string HELPTEXT = \
     "This program searches for and removes remnant adapter sequences from\n"
     "your read data.  The program can analyze both single end and paired end\n"

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