[mmseq] Rework compilation flags patch

[verdurin]

commit c6f5947946c579f045d965e8e5693a7cee930b27
Author: bloch at verdurin.com <bloch at verdurin.com>
Date:   Sun Mar 1 22:36:02 2015 +0000

    Rework compilation flags patch

 mmseq-flags.patch | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)
---
diff --git a/mmseq-flags.patch b/mmseq-flags.patch
index 6a8593d..6f0cf54 100644
--- a/mmseq-flags.patch
+++ b/mmseq-flags.patch
@@ -1,11 +1,11 @@
---- mmseq_0.9.14/src/Makefile	2011-09-20 11:27:55.000000000 +0100
-+++ mmseq_0.9.14.new/src/Makefile	2011-10-07 16:13:01.261226334 +0100
-@@ -35,7 +35,7 @@
- 	$(CXX) $(CXXFLAGS) -c sokal.cc
+diff -ur mmseq-1.0.8a/src/Makefile mmseq-1.0.8a-new/src/Makefile
+--- mmseq-1.0.8a/src/Makefile	2014-01-09 22:45:54.000000000 +0000
++++ mmseq-1.0.8a-new/src/Makefile	2015-03-01 22:35:22.349761703 +0000
+@@ -75,6 +75,7 @@
+ 	$(CXX) ${OPT} -c sokal.cc
  
  fasta.o : fasta.c fasta.h
--	$(CC) -c fasta.c
-+	$(CC) $(CXXFLAGS) -c fasta.c
++	$(CC) $(CXXFLAGS)  -c fasta.c
  
- bam2hits : fasta.o bam2hits.cpp
- 	${CXX} ${MACROS} $(CXXFLAGS) -fopenmp -O3 fasta.o bam2hits.cpp -o bam2hits ${LIBS_B2H}
+ uh.o : uh.cpp uh.hh
+ 	$(CXX) ${OMP} ${OPT} -c uh.cpp