Package: fermi-lite / 0.1+git20190320.b499514-1

Metadata

Package Version Patches format
fermi-lite 0.1+git20190320.b499514-1 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
make_shared_lib | (download)

Makefile | 9 7 + 2 - 0 !
1 file changed, 7 insertions(+), 2 deletions(-)

 build shared library
 Upstream only builds a static library, this adds a shared one.
hardening | (download)

Makefile | 15 6 + 9 - 0 !
1 file changed, 6 insertions(+), 9 deletions(-)

 add hardening flags
 Adds necessary build flags for hardening.
rename_bseq1_t.patch | (download)

README.md | 4 2 + 2 - 0 !
bfc.c | 18 9 + 9 - 0 !
bseq.c | 8 4 + 4 - 0 !
example.c | 4 2 + 2 - 0 !
fml.h | 14 7 + 7 - 0 !
internal.h | 2 1 + 1 - 0 !
misc.c | 10 5 + 5 - 0 !
7 files changed, 30 insertions(+), 30 deletions(-)

 avoid name space conflict with bwa
Bug-Upstream: https://github.com/lh3/fermi-lite/issues/5
bcf_seqlib.patch | (download)

bfc.c | 134 13 + 121 - 0 !
bfc.h | 153 153 + 0 - 0 !
2 files changed, 166 insertions(+), 121 deletions(-)

 try to take over patches from libseqlib which needs separate bfc.h
  FIXME: Please check the FIXME at the end.  I think I did things wrong to put a
         static declaration into header file but I had no better idea to make
         ec1buf_init known in libSeqLib
simde | (download)

ksw.c | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 use the simde header library for greater compatibility

ensure signed comparison.patch | (download)

mag.c | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 ensure that our variable checking for >= 0 is signed
 The type of v->n is size_t, which is an unsigned type, and we are assigning
 v->n - 1 to i and looping while this is >= 0.  If v->n == 0, on some
 architectures (armhf) this results in i being set to a positive value
 (specifically, UINT32_MAX).
sync_instead_of_atomic | (download)

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

 fix compatibility on mipsel
gcc10.patch | (download)

rle.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix package to build with gcc-10
Bug-Debian: https://bugs.debian.org/957198