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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-07-31 13:25:53 +0200 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-07-31 13:25:53 +0200 |
| commit | ca813e4a288c12c2fee6734cd97c73e86e129920 (patch) | |
| tree | 81e1dc7facebef46aff6653d3acd1d3caba695db /sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | |
| parent | sci-biology/ncbi-tools++: re-adding the patch with PCRE_LIBS added (diff) | |
| download | sci-ca813e4a288c12c2fee6734cd97c73e86e129920.tar.gz sci-ca813e4a288c12c2fee6734cd97c73e86e129920.tar.bz2 sci-ca813e4a288c12c2fee6734cd97c73e86e129920.zip | |
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/bwa-0.7.15-Makefile.patch')
| -rw-r--r-- | sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 |
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) |