Makefile | 19 10 + 9 - 0 !
1 file changed, 10 insertions(+), 9 deletions(-)

 use debian packaged libtabixpp

Makefile | 17 10 + 7 - 0 !
1 file changed, 10 insertions(+), 7 deletions(-)

 use debian packaged libsmithwaterman

src/multichoose.h | 79 79 + 0 - 0 !
1 file changed, 79 insertions(+)

 provide a needed header file

Makefile | 7 6 + 1 - 0 !
filevercmp/filevercmp.c | 180 180 + 0 - 0 !
filevercmp/filevercmp.h | 51 51 + 0 - 0 !
3 files changed, 237 insertions(+), 1 deletion(-)

 inject two files via quilt patch
 It would be better to use filevercmp module from gnulib package via
    gnulib-tool --import filevercmp
 but this would require configure.ac which is not (yet) done.
 .
 Upstream provides a copy of the code inside gnulib at
    https://github.com/ekg/filevercmp
 and thus it seems to be simpler to use this here at least for the moment.

Makefile | 20 8 + 12 - 0 !
1 file changed, 8 insertions(+), 12 deletions(-)

 use debian packaged libfastahack (and libdisorder)

Makefile | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 we provide a local copy of intervaltree in debian/include and
 inject it here in the build system

Makefile | 49 19 + 30 - 0 !
1 file changed, 19 insertions(+), 30 deletions(-)

 create shared lib instead of static

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

 there is a dir bin/ containing some r files which

Makefile | 8 1 + 7 - 0 !
1 file changed, 1 insertion(+), 7 deletions(-)

 use debian packaged libssw (while its not clear
 why two implementations of Smith-Waterman are needed at all)

libvcflib.pc | 11 11 + 0 - 0 !
1 file changed, 11 insertions(+)

 add pkg-config file to simplify building of freebayes

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

 the header file is named ssw_cpp.h

Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 upstream should use consistent installation target dir