sparsePregraph/Makefile | 2 1 + 1 - 0 !
sparsePregraph/inc/stdinc.h | 2 1 + 1 - 0 !
standardPregraph/Makefile | 2 1 + 1 - 0 !
standardPregraph/inc/stdinc.h | 1 1 + 0 - 0 !
4 files changed, 4 insertions(+), 3 deletions(-)

 use debian libraries instead of embedded headers

Makefile | 2 1 + 1 - 0 !
sparsePregraph/inc/multi_threads.h | 2 2 + 0 - 0 !
sparsePregraph/pregraph_sparse.cpp | 1 1 + 0 - 0 !
3 files changed, 4 insertions(+), 1 deletion(-)

 code from upstream fails to compile.
 An include is missing.
 Mail has been sent upstream and question posted to
 their google group but got no answer.

standardPregraph/main.c | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 usage show soapdenovo binary name
 while generated binaries are kmer dependent.
 Debian modification to lowercase applied too.

Makefile | 9 7 + 2 - 0 !
sparsePregraph/Makefile | 6 5 + 1 - 0 !
standardPregraph/Makefile | 9 7 + 2 - 0 !
3 files changed, 19 insertions(+), 5 deletions(-)

 makefile does not load cflags
 from env, add extra flags for debian fortify

standardPregraph/attachPEinfo.c | 2 1 + 1 - 0 !
standardPregraph/hashFunction.c | 6 3 + 3 - 0 !
standardPregraph/inc/extfunc.h | 4 2 + 2 - 0 !
standardPregraph/kmer.c | 4 2 + 2 - 0 !
standardPregraph/loadPreGraph.c | 2 1 + 1 - 0 !
standardPregraph/node2edge.c | 12 6 + 6 - 0 !
standardPregraph/orderContig.c | 2 1 + 1 - 0 !
standardPregraph/output_pregraph.c | 2 1 + 1 - 0 !
standardPregraph/prlRead2Ctg.c | 10 5 + 5 - 0 !
standardPregraph/prlReadFillGap.c | 4 2 + 2 - 0 !
10 files changed, 24 insertions(+), 24 deletions(-)

 debian library is more recent than the one embedded upstream.
 Its API changed and code needs to be updated to use this version.
 See more info here:
 http://www.postgresql.org/message-id/1329988571.6474.9.camel@vanquo.pezone.net

sparsePregraph/Makefile | 1 1 + 0 - 0 !
sparsePregraph/main.cpp | 2 1 + 1 - 0 !
sparsePregraph/pregraph_sparse.cpp | 2 1 + 1 - 0 !
standardPregraph/Makefile | 1 1 + 0 - 0 !
standardPregraph/main.c | 2 1 + 1 - 0 !
5 files changed, 5 insertions(+), 3 deletions(-)

 enable reproducible build