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| author |   David Seifert <soap@gentoo.org> | 2020-09-26 12:00:45 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2020-09-26 12:00:45 +0200 |
| commit | 11e7107dfc5e8b95c3af3887c388fa1272b8ddb2 (patch) | |
| tree | 1b285d6d68c121c2e89eaf70c81746bd031ab74e /sci-biology/bwa/files | |
| parent | app-text/ghostscript-gpl: bump to v9.53.2 (diff) | |
| download | gentoo-11e7107dfc5e8b95c3af3887c388fa1272b8ddb2.tar.gz gentoo-11e7107dfc5e8b95c3af3887c388fa1272b8ddb2.tar.bz2 gentoo-11e7107dfc5e8b95c3af3887c388fa1272b8ddb2.zip | |
sci-biology/bwa: Bump version to 0.7.17
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology/bwa/files')
| -rw-r--r-- | sci-biology/bwa/files/bwa-0.7.17-Makefile.patch | 42 | ||||
| -rw-r--r-- | sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch | 11 |
2 files changed, 53 insertions, 0 deletions
diff --git a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch new file mode 100644 index 000000000000..944369cb75e2 --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch @@ -0,0 +1,42 @@ +--- a/Makefile ++++ b/Makefile +@@ -1,9 +1,7 @@ +-CC= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++CFLAGS+= -Wall -Wno-unused-function + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar +-DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) ++CPPFLAGS+= -DHAVE_PTHREAD $(WRAP_MALLOC) + LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \ + QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o + AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ +@@ -21,16 +19,13 @@ + + .SUFFIXES:.c .o .cc + +-.c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ +- + all:$(PROG) + + bwa:libbwa.a $(AOBJS) main.o +- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) + + bwamem-lite:libbwa.a example.o +- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS) + + libbwa.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) +@@ -39,7 +34,7 @@ + rm -f gmon.out *.o a.out $(PROG) *~ *.a + + depend: +- ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c ) ++ ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c ) + + # DO NOT DELETE THIS LINE -- make depend depends on it. + diff --git a/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch new file mode 100644 index 000000000000..1babb8356c4a --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch @@ -0,0 +1,11 @@ +--- a/rle.h ++++ b/rle.h +@@ -30,7 +30,7 @@ + *** 43+3 codec *** + ******************/ + +-const uint8_t rle_auxtab[8]; ++extern const uint8_t rle_auxtab[8]; + + #define RLE_MIN_SPACE 18 + #define rle_nptr(block) ((uint16_t*)(block)) |