src/task_break.cpp | 2 1 + 1 - 0 !
src/task_fcdrate.cpp | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 small spelling fix

src/Makefile | 25 12 + 13 - 0 !
src/reapr.pl | 4 2 + 2 - 0 !
src/task_break.cpp | 1 0 + 1 - 0 !
src/task_fcdrate.cpp | 1 0 + 1 - 0 !
src/task_perfectfrombam.pl | 6 3 + 3 - 0 !
src/task_perfectmap.pl | 8 4 + 4 - 0 !
src/task_pipeline.pl | 2 1 + 1 - 0 !
src/task_plots.pl | 6 3 + 3 - 0 !
src/task_preprocess.pl | 6 3 + 3 - 0 !
src/task_score.cpp | 1 0 + 1 - 0 !
src/task_seqrename.pl | 2 1 + 1 - 0 !
src/task_smaltmap.pl | 4 2 + 2 - 0 !
src/task_stats.cpp | 1 0 + 1 - 0 !
src/utils.h | 2 1 + 1 - 0 !
14 files changed, 32 insertions(+), 37 deletions(-)

 use_shared_libs

src/Makefile | 70 35 + 35 - 0 !
1 file changed, 35 insertions(+), 35 deletions(-)

 hardening

src/task_smaltmap.pl | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 adapt samtools sort usage to 1.3 syntax 
 Samtools 1.3 changed the syntax of the 'samtools sort' command, breaking
 REAPR's smaltmap command in the process.
 Discussed and forwarded to upstream in person, hence no URL.

src/Makefile | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 rearrange linking order to fix ftbfs with ld --as-needed
 Thanks to Logan Rosen <logan@ubuntu.com> for the patch.