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jlec 14/10/02 10:25:34 |
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Added: Bio-SamTools-1.390.0-samtools-1.patch |
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Log: |
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dev-perl/Bio-SamTools: Make it build with samtools-1, #523568 |
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(Portage version: 2.2.14_rc1/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
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Revision Changes Path |
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1.1 dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch?rev=1.1&content-type=text/plain |
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Index: Bio-SamTools-1.390.0-samtools-1.patch |
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=================================================================== |
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Build.PL | 2 +- |
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c_bin/makefile | 6 +++--- |
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lib/Bio/DB/Sam.xs | 9 ++++++--- |
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3 files changed, 10 insertions(+), 7 deletions(-) |
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|
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diff --git a/Build.PL b/Build.PL |
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index 1393e03..cf97ad5 100644 |
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--- a/Build.PL |
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+++ b/Build.PL |
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@@ -38,7 +38,7 @@ my $build = $class->new( |
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dist_abstract => 'Perl interface to SamTools library for DNA sequencing', |
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license => 'perl', |
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include_dirs => [$sam_include], |
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- extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'], |
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+ extra_linker_flags => ["-L$sam_lib",'-lbam','-lhts','-lpthread','-lz'], |
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|
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extra_compiler_flags=>[ |
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|
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diff --git a/c_bin/makefile b/c_bin/makefile |
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index 9aef917..96a30f2 100644 |
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--- a/c_bin/makefile |
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+++ b/c_bin/makefile |
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@@ -1,5 +1,5 @@ |
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-CC= gcc |
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-CFLAGS= -g -Wall -O2 -fPIC |
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+CC?= gcc |
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+CFLAGS?= -g -Wall -O2 -fPIC |
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DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 |
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INCLUDES= |
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LIBPATH= |
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@@ -14,7 +14,7 @@ PROG= bam2bedgraph |
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all:$(PROG) |
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|
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bam2bedgraph: bam2bedgraph.o |
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- $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lpthread -lm -lz |
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+ $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lhts -lpthread -lm -lz |
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|
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clean: |
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rm -f *.o $(PROG) |
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diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs |
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index 5ca303b..7f92860 100644 |
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--- a/lib/Bio/DB/Sam.xs |
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+++ b/lib/Bio/DB/Sam.xs |
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@@ -571,9 +571,12 @@ bama_l_aux(b,...) |
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Bio::DB::Bam::Alignment b |
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PROTOTYPE: $;$ |
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CODE: |
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- if (items > 1) |
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- b->l_aux = SvIV(ST(1)); |
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- RETVAL=b->l_aux; |
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+ if (items > 1) { |
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+ RETVAL = SvIV(ST(1)); |
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+ } |
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+ else { |
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+ RETVAL=bam_get_l_aux(b); |
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+ } |
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OUTPUT: |
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RETVAL |
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