Package: staden-io-lib / 1.14.11-6

Metadata

Package Version Patches format
staden-io-lib 1.14.11-6 3.0 (quilt)

Patch series

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

io_lib/cram_index.c | 8 8 + 0 - 0 !
io_lib/cram_io.c | 8 8 + 0 - 0 !
io_lib/files.c | 8 8 + 0 - 0 !
io_lib/srf.h | 8 8 + 0 - 0 !
progs/cram_index.c | 8 8 + 0 - 0 !
5 files changed, 40 insertions(+)

 define path_max in case it is not available
             this is needed to compile on hurd_i386

fix_fseeko.patch | (download)

io_lib/bgzip.c | 4 4 + 0 - 0 !
1 file changed, 4 insertions(+)

 attempt to fix ftbfs on non-i386 32bit for fseeko()


fix_non_x86.patch | (download)

io_lib/bam.c | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 [patch] bug fix to scramble on systems not defining allow_uac.

(Mostly non-Intel platforms.)

remove_bashism.patch | (download)

tests/scram.test | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 remove bashism in test script
Bug-Debian: https://bugs.debian.org/915460
d4591b5.patch | (download)

io_lib/bam.c | 52 27 + 25 - 0 !
1 file changed, 27 insertions(+), 25 deletions(-)

 [patch] big endian fix for bam reading.

Fixes Debian Bug#915450

37b33d3.patch | (download)

io_lib/bam.h | 3 2 + 1 - 0 !
io_lib/cram_decode.c | 9 5 + 4 - 0 !
2 files changed, 7 insertions(+), 5 deletions(-)

 [patch] bug multi-threaded cram decode on some systems.

The bulk_cram_to_bam function allocated a large array for the BAM
objects, but did not ensure the bam structures are aligned on a word
boundary.  This gave rise to bus errors.  Fixes debian Bug#915459

1b28b6a.patch | (download)

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

 [patch] fix rans codec on x32 architecture.

This is 32-bit usage of a 64-bit processor.  See
https://wiki.debian.org/X32Port
Should fix the bug found here:
https://buildd.debian.org/status/fetch.php?pkg=staden-io-lib&arch=x32&ver=1.14.11-3&stamp=1543952038&raw=0

242cd6b.patch | (download)

io_lib/hash_table.c | 10 5 + 5 - 0 !
1 file changed, 5 insertions(+), 5 deletions(-)

 [patch] fix hash table hash_int_keys on 32-bit platforms

The hash table has the option to declare the key pointer is the key
itself rather than the memory it points to.  It assumed however that
the key was 8 bytes long, rather than sizeof(char *).

Fixes Debian Bug#915460

serial tests.patch | (download)

configure.in | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 use serial tests


spelling | (download)

io_lib/mach-io.c | 2 1 + 1 - 0 !
io_lib/mach-io.h | 2 1 + 1 - 0 !
io_lib/seqIOABI.c | 2 1 + 1 - 0 !
io_lib/seqIOALF.c | 2 1 + 1 - 0 !
4 files changed, 4 insertions(+), 4 deletions(-)

 spelling: independant→independent