Merge develop to master, end-of-sprint 2018.10 05/23/2018 (@...

Merge develop to master, end-of-sprint 2018.10 05/23/2018 (@ smrtlink-short_5_2_0_snapshot36228, RBS-DEVSMRTLINKSHORT-2801)

bamboo_coverage.sh

+#!/usr/bin/env bash
+set -xve
+
+source /mnt/software/Modules/current/init/bash
+module load gcc meson ccache ninja zlib htslib samtools cram boost gtest gcov
+
+echo "#####################"
+echo "# BUILD & RUN TESTS #"
+echo "#####################"
+
+rm -rf build
+mkdir build 
+cd build
+
+meson \
+  --werror \
+  --backend ninja \
+  --buildtype debug \
+  --default-library shared \
+  --libdir lib \
+  --wrap-mode nofallback \
+  --prefix "${PREFIX_ARG:-/usr/local}" \
+  -Db_coverage=true \
+  ..
+
+ninja test
+
+echo "################"
+echo "# COVERAGE     #"
+echo "################"
+
+find . -type f -iname '*.o' | xargs gcov -acbrfu {} \; >/dev/null && \
+mkdir coverage && pushd coverage && mv ../*.gcov . && \
+sed -i -e 's@Source:@Source:../@' *.gcov && \
+sed -i -e 's@Graph:@Graph:../@' *.gcov && \
+sed -i -e 's@Data:@Data:../@' *.gcov && \
+rm pugixml*
+