sci-biology/yaha: Fix build with gcc-5 and respect build tools

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <[email protected]>

sci-biology/yaha/files/yaha-9999-buildsystem.patch

@@ -0,0 +1,61 @@
+diff --git a/Makefile b/Makefile
+index 44fa872..b844ba6 100644
+--- a/Makefile
++++ b/Makefile
+@@ -10,24 +10,27 @@ SDIR := src
+ ODIR := obj
+ BDIR := bin
+
++CC	     ?= gcc
++CXX      ?= g++
++CFLAGS   ?= -Wall -O3
++CXXFLAGS ?= -Wall -O3
++LDFLAGS  ?=
++
++CFLAGS	 += -MMD -MP -std=gnu99
++CXXFLAGS += -MMD -MP
++LDFLAGS  += -pthread
++
+ # Set up flags depending on mode
+ ifdef USERMODE
+ PROG	 := yaha
+-CCFLAGS  := -Wall -O3 -D COMPILE_USER_MODE -D BUILDNUM=$(BUILDNUM)
++CFLAGS   += -D COMPILE_USER_MODE -D BUILDNUM=$(BUILDNUM)
++CXXFLAGS += -D COMPILE_USER_MODE -D BUILDNUM=$(BUILDNUM)
+ else
+ PROG	 := yaha$(BUILDNUM)
+-CCFLAGS  := -Wall -Winline -O3 -g -D BUILDNUM=$(BUILDNUM)
++CFLAGS   += -g -D BUILDNUM=$(BUILDNUM)
++CXXFLAGS += -g -D BUILDNUM=$(BUILDNUM)
+ endif
+
+-# Auto build dependency files.
+-CCFLAGS  += -MMD -MP
+-
+-CC	 := gcc
+-CPP      := g++
+-CFLAGS	 := $(CCFLAGS) -std=gnu99
+-CPPFLAGS := $(CCFLAGS)
+-LDFLAGS  := -pthread
+-
+ # The list of object files.
+ OBJfiles := Main.o AlignArgs.o AlignHelpers.o AlignExtFrag.o AlignOutput.o BaseSeq.o Compress.o \
+ 	FileHelpers.o GraphPath.o Index.o Query.o QueryMatch.o QueryState.o SW.o Math.o
+@@ -45,7 +48,7 @@ $(BDIR):
+
+ # Link the program
+ $(BDIR)/$(PROG): $(OBJS)
+-	$(CPP) $(LDFLAGS) -o $@ $(OBJS)
++	$(CXX) $(LDFLAGS) -o $@ $(OBJS)
+
+ # Include the dependencies.
+ # The actual objects will be built by the below generic rules based on these dependencies.
+@@ -58,7 +61,7 @@ $(ODIR)/%.o: $(SDIR)/%.c
+ 	$(CC) $(CFLAGS) -c $< -o $@
+
+ $(ODIR)/%.o: $(SDIR)/%.cpp
+-	$(CPP) $(CPPFLAGS) -c $< -o $@
++	$(CXX) $(CXXFLAGS) -c $< -o $@
+
+ .PHONY: clean
+ clean:

sci-biology/yaha/files/yaha-9999-fpermissive.patch

@@ -0,0 +1,16 @@
+ src/SW.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/SW.cpp b/src/SW.cpp
+index 57d2773..3a9c225 100644
+--- a/src/SW.cpp
++++ b/src/SW.cpp
+@@ -796,7 +796,7 @@ int findAGSBackwardExtensionCarefully(QueryState_t * QS,  ROFF rOff, char * qStr
+ ////////////////////////
+
+ template <BOOL banded, BOOL extension, BOOL reverse, BOOL XCutoff>
+-int findAffineGapScore(QueryState_t * QS, char * qStr, SUINT qLen, char * rStr, SUINT rLen, EditOpList_t * list, SUINT * addedQLen = NULL, SUINT * addedRLen = NULL)
++int findAffineGapScore(QueryState_t * QS, char * qStr, SUINT qLen, char * rStr, SUINT rLen, EditOpList_t * list, SUINT * addedQLen, SUINT * addedRLen)
+ {
+     // As we will go row by row, then column by column, we do not need to store all of the V, E, and F arrays.
+     // Instead we will store only the previous row and column for each.

sci-biology/yaha/yaha-9999.ebuild

@@ -4,7 +4,7 @@
 
 EAPI=6
 
-inherit git-r3
+inherit flag-o-matic git-r3 toolchain-funcs
 
 DESCRIPTION="DNA mapper for single-end reads to detect structural variants (SV)"
 HOMEPAGE="https://github.com/GregoryFaust/yaha"
@@ -15,11 +15,19 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
+PATCHES=(
+	"${FILESDIR}"/${P}-fpermissive.patch
+	"${FILESDIR}"/${P}-buildsystem.patch
+)
 
-# TODO: respect CFLAGS/CXXFLAGS
-# https://github.com/GregoryFaust/yaha/issues/5
+src_prepare() {
+	default
+	append-cflags '-DCOMPILE_USER_MODE' '-DBUILDNUM=$(BUILDNUM)' -std=gnu99
+	append-cxxflags '-DCOMPILE_USER_MODE' '-DBUILDNUM=$(BUILDNUM)'
+	tc-export CC CXX
+	export CFLAGS
+	export CXXFLAGS
+}
 
 src_install(){
 	dobin bin/yaha