[Debian-med-packaging] Bug#844034: Any intend to fix this soon

[Andreas Tille]

On Sat, Dec 24, 2016 at 02:39:03PM +0100, Andreas Tille wrote:
> Hi again,

once more.  I just noticed that blasr 5.3-2 is properly linked and bhoney
test suite works now ...
 
> On Sat, Dec 24, 2016 at 10:30:48AM +0100, Andreas Tille wrote:
> > pbhoney is marked for autoremoval due to this bug.  I'm guessing from
> > the description of the problem that it should be easy to fix (without
> > having checked).  Do you intend to upload soon or should somebody
> > else step in here?
> 
> I've spent some time to work on this.  I admit its pretty confusing to
> parse blasr code what options are really used.  I've tried some trial
> and error approach and I think I've got the options now somehow working.
> However, when trying the first command from the test suite I get:
> 
> 
> $ /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam
> 
> Please Cite: English, Adam C., William J. Salerno, Jeffery G.
>              Reid. "PBHoney: identyfying genomic variants via
>              long-read discordance and interrupted mapping."
>              BMC Bioinformatics 2014, 15:180 (June 10, 2014).
>              doi:10.1186/1471-2105-15-180
> 
> 2016-12-24 14:29:32,478 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam
> 2016-12-24 14:29:32,478 [INFO] Running Blasr
> 2016-12-24 14:29:32,489 [ERROR] blasr mapping failed!
> 2016-12-24 14:29:32,489 [ERROR] RETCODE 134
> 2016-12-24 14:29:32,489 [ERROR] STDOUT [INFO] 2016-12-24T14:29:32 [blasr] started.
> blasr: iblasr/MappingParameters.h:584: void MappingParameters::MakeSane(): Assertion `"blasr must be compiled with lib pbbam to perform IO on bam." == 0' failed.
> Aborted
> 
> 2016-12-24 14:29:32,489 [ERROR] STDERR None
> 2016-12-24 14:29:32,489 [ERROR] Exiting
> 
> 
> To verify whether blasr is linked against libpbbam I did:
> 
>   $ ldd /usr/bin/blasr | grep libpbbam
> 
> I'm not really sure how to continue from here.
> 
> Kind regards
> 
>        Andreas.
> 
> -- 
> http://fam-tille.de

-- 
http://fam-tille.de