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

[Andreas Tille]

Hi again,

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.

-- 
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