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.
--
http://fam-tille.de
