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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-07-31 13:25:53 +0200
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-07-31 13:25:53 +0200
commitca813e4a288c12c2fee6734cd97c73e86e129920 (patch)
tree81e1dc7facebef46aff6653d3acd1d3caba695db /sci-biology/bwa/files
parentsci-biology/ncbi-tools++: re-adding the patch with PCRE_LIBS added (diff)
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sci-biology/bwa: version bump
Release 0.7.16 (30 July 2017) ----------------------------- This release added a couple of minor features and incorporated multiple pull requests, including: * Added option -5, which is useful to some Hi-C pipelines. * Fixed an error with samtools sorting (#129). Updated download link for GRCh38 (#123). Fixed README MarkDown formatting (#70). Addressed multiple issues via a collected pull request #139 by @jmarshall. Avoid malformatted SAM header when -R is used with TAB (#84). Output mate CIGAR (#138). This release is expected to give the same alignment as 0.7.15, except the added mate-cigar tag. (0.7.16: 30 July 2017, r1180) https://lists.sourceforge.net/lists/listinfo/bio-bwa-help Package-Manager: Portage-2.3.6, Repoman-2.3.3
Diffstat (limited to 'sci-biology/bwa/files')
-rw-r--r--sci-biology/bwa/files/bwa-0.7.15-Makefile.patch27
1 files changed, 27 insertions, 0 deletions
diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
new file mode 100644
index 000000000..39b437a02
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
@@ -0,0 +1,27 @@
+--- bwa-0.7.13/Makefile
++++ bwa-0.7.13/Makefile
+@@ -1,8 +1,8 @@
+-CC= gcc
++CC?= gcc
+ #CC= clang --analyze
+-CFLAGS= -g -Wall -Wno-unused-function -O2
++CFLAGS?= -g -Wall -Wno-unused-function -O2
+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+-AR= ar
++AR?= ar
+ DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
+ LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
+ AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
+@@ -26,10 +26,10 @@
+ all:$(PROG)
+
+ bwa:libbwa.a $(AOBJS) main.o
+- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+
+ bwamem-lite:libbwa.a example.o
+- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+
+ libbwa.a:$(LOBJS)
+ $(AR) -csru $@ $(LOBJS)