src/segment_juncs.cpp | 11 7 + 4 - 0 !
1 file changed, 7 insertions(+), 4 deletions(-)

---

configure.ac | 2 1 + 1 - 0 !
src/align_status.h | 2 1 + 1 - 0 !
src/bam2fastx.cpp | 4 2 + 2 - 0 !
src/bwt_map.h | 2 1 + 1 - 0 !
src/common.h | 4 2 + 2 - 0 !
src/map2gtf.h | 4 2 + 2 - 0 !
6 files changed, 9 insertions(+), 9 deletions(-)

 corrected location for samtools .h files 

src/tophat2.in | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

---

src/samtools-0.1.18/Makefile | 6 4 + 2 - 0 !
1 file changed, 4 insertions(+), 2 deletions(-)

 add hardening flags to embedded copy of samtools