CMakeLists.txt | 145 101 + 44 - 0 !
1 file changed, 101 insertions(+), 44 deletions(-)

 link against system libraries

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

 deactivate multi-threaded writing

VariantCaller/Bookkeeping/ExtendParameters.cpp | 6 5 + 1 - 0 !
1 file changed, 5 insertions(+), 1 deletion(-)

 small style change to display usage information

Util/Utils.cpp | 6 4 + 2 - 0 !
1 file changed, 4 insertions(+), 2 deletions(-)

 replace path_max with hardcoded value to avoid build error on hurd

BaseCaller/TreephaserSSE.cpp | 47 1 + 46 - 0 !
1 file changed, 1 insertion(+), 46 deletions(-)

 remove sse guards

CMakeLists.txt | 12 2 + 10 - 0 !
1 file changed, 2 insertions(+), 10 deletions(-)

 use debian packaged libsmithwaterman

bin/variant_caller_pipeline.py | 6 3 + 3 - 0 !
external/vcflib/multichoose/multipermute.py | 8 4 + 4 - 0 !
2 files changed, 7 insertions(+), 7 deletions(-)

---

external/freebayes/src/AlleleParser.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 declare operator as const to fix gcc11 ftbfs