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| author |   Kent Fredric <kentnl@gentoo.org> | 2018-04-05 12:02:29 +1200 |
|---|---|---|
| committer | Kent Fredric <kentnl@gentoo.org> | 2018-04-15 20:35:26 +1200 |
| commit | b00fcf2f5384095b7e41c5966adac26a05b6ce67 (patch) | |
| tree | 879ddeba8ca63bf0c503f3e6bb64157d00246f23 /dev-perl/Bio-SamTools/files | |
| parent | dev-perl/Bio-Das: Cleanup old (diff) | |
| download | gentoo-b00fcf2f5384095b7e41c5966adac26a05b6ce67.tar.gz gentoo-b00fcf2f5384095b7e41c5966adac26a05b6ce67.tar.bz2 gentoo-b00fcf2f5384095b7e41c5966adac26a05b6ce67.zip | |
dev-perl/Bio-SamTools: Cleanup old
Package-Manager: Portage-2.3.24, Repoman-2.3.6
Diffstat (limited to 'dev-perl/Bio-SamTools/files')
| -rw-r--r-- | dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch | 59 |
1 files changed, 0 insertions, 59 deletions
diff --git a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch deleted file mode 100644 index 8e7250c51736..000000000000 --- a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch +++ /dev/null @@ -1,59 +0,0 @@ - Build.PL | 2 +- - c_bin/makefile | 6 +++--- - lib/Bio/DB/Sam.xs | 9 ++++++--- - 3 files changed, 10 insertions(+), 7 deletions(-) - -diff --git a/Build.PL b/Build.PL -index 1393e03..cf97ad5 100644 ---- a/Build.PL -+++ b/Build.PL -@@ -38,7 +38,7 @@ my $build = $class->new( - dist_abstract => 'Perl interface to SamTools library for DNA sequencing', - license => 'perl', - include_dirs => [$sam_include], -- extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'], -+ extra_linker_flags => ["-L$sam_lib",'-lbam','-lhts','-lpthread','-lz'], - - extra_compiler_flags=>[ - -diff --git a/c_bin/makefile b/c_bin/makefile -index 9aef917..96a30f2 100644 ---- a/c_bin/makefile -+++ b/c_bin/makefile -@@ -1,5 +1,5 @@ --CC= gcc --CFLAGS= -g -Wall -O2 -fPIC -+CC?= gcc -+CFLAGS?= -g -Wall -O2 -fPIC - DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 - INCLUDES= - LIBPATH= -@@ -14,7 +14,7 @@ PROG= bam2bedgraph - all:$(PROG) - - bam2bedgraph: bam2bedgraph.o -- $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lpthread -lm -lz -+ $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lhts -lpthread -lm -lz - - clean: - rm -f *.o $(PROG) -diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs -index 5ca303b..7f92860 100644 ---- a/lib/Bio/DB/Sam.xs -+++ b/lib/Bio/DB/Sam.xs -@@ -571,9 +571,12 @@ bama_l_aux(b,...) - Bio::DB::Bam::Alignment b - PROTOTYPE: $;$ - CODE: -- if (items > 1) -- b->l_aux = SvIV(ST(1)); -- RETVAL=b->l_aux; -+ if (items > 1) { -+ RETVAL = SvIV(ST(1)); -+ } -+ else { -+ RETVAL=bam_get_l_aux(b); -+ } - OUTPUT: - RETVAL - |