[Debian-med-packaging] Bug#851764: src:hhsuite: type mismatch in printf(3); affects manpage

[Daniel Shahaf]

Package: hhsuite
Version: 3.0~beta2+dfsg-1
Severity: minor
Tags: upstream patch
User: reproducible-builds at lists.alioth.debian.org
Usertags: randomness

Dear Maintainer,

hhblits.cpp uses the %i printf(3) conversion to format a 'double' value:

src/hhblits.cpp:333:    printf(" -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=%i)\n", par.prefilter_evalue_thresh);

Formally that's undefined behaviour, although in practice it simply
prints a garbage value.  That garbage value is also embedded into the
hhblits_omp(1) man page. 

Furthermore, hhsuite-userguide.tex specifies the default value as '0'
whereas the code uses '1000'.

The attached patch should fix both issues.

Cheers,

Daniel

P.S. ViterbiRunner::calculateEarlyStop() puts the return value of log(3)
into a 'float' variable, even though that function returns double.  I'm
not sure whether that's intentional or what effect it may have.