Package: libseqlib / 1.1.2+dfsg-1~bpo9+1

Metadata

Package Version Patches format
libseqlib 1.1.2+dfsg-1~bpo9+1 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
use_debian_packaged_libs.patch | (download)

Makefile.am | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 skip subdirs in favour of debian packaged development
 libraries and do not use broken install target


adapt_to_debian_fermi lite.patch | (download)

SeqLib/BFC.h | 2 1 + 1 - 0 !
SeqLib/FermiAssembler.h | 2 1 + 1 - 0 !
src/BFC.cpp | 11 6 + 5 - 0 !
src/FermiAssembler.cpp | 16 8 + 8 - 0 !
4 files changed, 16 insertions(+), 15 deletions(-)

 in debian's fermi-lite 0.1-3 a name space pollution with
fix_fermi lite_usage.patch | (download)

SeqLib/BFC.h | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 upstream tries to include a header file bfc.h which
 can not be found in fermi-lite.  Just skip this.
 .
 Also use system installed libfml-dev header file.


fix_htslib_usage.patch | (download)

SeqLib/BamHeader.h | 8 4 + 4 - 0 !
SeqLib/BamRecord.h | 10 5 + 5 - 0 !
SeqLib/RefGenome.h | 2 1 + 1 - 0 !
src/ReadFilter.cpp | 2 1 + 1 - 0 !
4 files changed, 11 insertions(+), 11 deletions(-)

 use header files from libhts-dev


fml_include_path.patch | (download)

SeqLib/FermiAssembler.h | 6 3 + 3 - 0 !
seq_test/Makefile.am | 7 2 + 5 - 0 !
src/Makefile.am | 2 1 + 1 - 0 !
3 files changed, 6 insertions(+), 9 deletions(-)

 make sure header files will be found in /usr/include/fml


dynamic_lib.patch | (download)

configure.ac | 6 6 + 0 - 0 !
src/Makefile.am | 7 4 + 3 - 0 !
2 files changed, 10 insertions(+), 3 deletions(-)

 create dynamic library


use_debian_packaged_jsoncpp.patch | (download)

seq_test/Makefile.am | 2 1 + 1 - 0 !
src/Makefile.am | 4 2 + 2 - 0 !
2 files changed, 3 insertions(+), 3 deletions(-)

 do not use code copy of jsoncpp


use_debian_packaged_ssw.patch | (download)

seq_test/Makefile.am | 2 1 + 1 - 0 !
src/BamRecord.cpp | 2 1 + 1 - 0 !
src/Makefile.am | 2 1 + 1 - 0 !
3 files changed, 3 insertions(+), 3 deletions(-)

 do not use code copy of libssw


pkg config.patch | (download)

Makefile.am | 4 4 + 0 - 0 !
configure.ac | 4 3 + 1 - 0 !
libseqlib.pc.in | 11 11 + 0 - 0 !
3 files changed, 18 insertions(+), 1 deletion(-)

 add pkg-config file


use_private_htslib_headers.patch | (download)

SeqLib/BamWalker.h | 4 2 + 2 - 0 !
libseqlib.pc.in | 2 1 + 1 - 0 !
2 files changed, 3 insertions(+), 3 deletions(-)

 hack around improper use of private files of htslib