Your message dated Thu, 31 Aug 2017 22:34:32 +0000
with message-id <[email protected]>
and subject line Bug#871697: fixed in jellyfish 2.2.6-5
has caused the Debian Bug report #871697,
regarding jellyfish: Please add arm64
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
871697: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=871697
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: jellyfish
Version: 2.2.6-1
User: [email protected]
Usertags: arm64
Jellyfish seems to be easy to port. Just provide alternatives to the
inline assembler in rectangular_binary_matrix.hpp:
#ifdef __x86_64__
#define AND_XOR(off) \
asm("movdqa (%[s],%[i]), %[load]\n\t" \
"pand " #off "(%[p]),%[load]\n\t" \
"pxor %[load],%[acc]\n\t" \
: [acc]"=&x"(acc) \
: "[acc]"(acc), [i]"r"(i), [p]"r"(p), [s]"r"(smear), [load]"x"(load))
#else
#define AND_XOR(off) do { \
xmm_t a = { smear[i / 8], smear[i / 8 + 1] }; \
xmm_t b = { p[(off) / 8], p[(off) / 8 + 1] }; \
acc ^= a & b; \
} while (0)
#endif
#ifdef __x86_64__
uint64_t res1, res2;
asm("movd %[acc], %[res1]\n\t"
"psrldq $8, %[acc]\n\t"
"movd %[acc], %[res2]\n\t"
: [res1]"=r"(res1), [res2]"=r"(res2)
: [acc]"x"(acc));
return res1 ^ res2;
#else
return acc[0] ^ acc[1];
#endif
Then replace AND_XOR("0x30") with AND_XOR(0x30), AND_XOR("") with
AND_XOR(0), and so on.
You might find the non-assembler version performs just as well on amd64, too,
in which case you could simplify the code.
Tested on arm64. Likely to work on some other architectures.
--- End Message ---
--- Begin Message ---
Source: jellyfish
Source-Version: 2.2.6-5
We believe that the bug you reported is fixed in the latest version of
jellyfish, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated jellyfish package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 01 Sep 2017 00:09:35 +0200
Source: jellyfish
Binary: jellyfish libjellyfish-2.0-2 libjellyfish-2.0-dev python3-dna-jellyfish
libjellyfish-perl jellyfish-examples
Architecture: source
Version: 2.2.6-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
jellyfish - count k-mers in DNA sequences
jellyfish-examples - count k-mers in DNA sequences (examples for testing)
libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of
jellyfish)
libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of
jellyfish)
libjellyfish-perl - count k-mers in DNA sequences (Perl bindings of jellyfish)
python3-dna-jellyfish - count k-mers in DNA sequences (Python bindings of
jellyfish)
Closes: 871697
Changes:
jellyfish (2.2.6-5) unstable; urgency=medium
.
* Make jellyfish portable (Thanks for the patch to Edmund Grimley Evans
<[email protected]>)
Closes: #871697
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