CMakeLists.txt | 390 195 + 195 - 0 !
src/CMakeLists.txt | 33 15 + 18 - 0 !
2 files changed, 210 insertions(+), 213 deletions(-)

 use debian version of dependencies, don't download them

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

 fix upstream's typos

src/Salmon.cpp | 8 4 + 4 - 0 !
1 file changed, 4 insertions(+), 4 deletions(-)

 disable the newer version check

CMakeLists.txt | 6 5 + 1 - 0 !
1 file changed, 5 insertions(+), 1 deletion(-)

 use pkgconfig to find the system library for tbb

CMakeLists.txt | 2 1 + 1 - 0 !
src/CMakeLists.txt | 6 1 + 5 - 0 !
2 files changed, 2 insertions(+), 6 deletions(-)

 remove unnecessarily linked libraries

src/CMakeLists.txt | 11 3 + 8 - 0 !
1 file changed, 3 insertions(+), 8 deletions(-)

 remove salmon_core lib

CMakeLists.txt | 84 42 + 42 - 0 !
1 file changed, 42 insertions(+), 42 deletions(-)

 remove find_package for liblzma and libbz2

As these seem not to be required.

CMakeLists.txt | 2 1 + 1 - 0 !
src/CMakeLists.txt | 24 12 + 12 - 0 !
2 files changed, 13 insertions(+), 13 deletions(-)

 use debian packaged rapmap
 Currently RapMap sources need to be embedded, see
 https://github.com/COMBINE-lab/salmon/issues/87 for a discussion
 with upstream. 

src/SalmonQuantify.cpp | 2 2 + 0 - 0 !
1 file changed, 2 insertions(+)

 redefine mem_f_self_ovlp
 libbwa upstream has dropped MEM_F_SELF_OVLP in their commit 
 1247dc234668c1d7357fa6343222e9b5730e832d. This patch re-introduces this
 definition to fix an FTBFS.

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

 fix path of unittest executable

CMakeLists.txt | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 make build reproducible
 Not fully reproducible yet as instances of __FILE__ still contain
 build directory.