feat: errors are emitted from asyncronous tasks #25
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In the `align` function (`align.jl`) - added `@sync` macro on the loop in which threads are spawned. - removed the try-catch (obsolete?)
replace with just a local variable
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This looks good to me. I think try it on a few more cases and merge it. It's a rather essential fix so should take top priority. |
this channel was used to return the final graph, and is now not needed anymore.
alignment tasks that run in parallel have a try-catch statement. If an error occurs, it is passed to an error channel, together with the stacktrace. The main thread waits on this error channel, and logs any error received and throws a new error. The error channel is closed in the last alignment taks, when the root graph is created.
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With this last commit now this looks good to me. If errors occur in any of the alignment tasks, they are passed on an error channel to the main thread. The main threads logs the error and stacktrace on stderr, and then throws a new error, stopping the execution. |
mmolari
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Oct 12, 2022
## Changes: - added [mmseqs2](https://github.com/soedinglab/MMseqs2) as an alternative alignment kernel that guarantees higher sensitivity at the expense of longer computational time, see [#33](#33). - updated Docker file to include mmseqs2 in the container. - updated the documentation, including discussion of alignment kernel sensitivities and examples of application of PanGraph to plasmids by [@liampshaw](https://github.com/neherlab/pangraph/commits?author=liampshaw). - errors that occur in worker threads are now emitted on the main thread, see [#25](#25). - fixed a bug in detransitive, see this [commit](a965132) - added snakemake pipeline in the `script` folder to perform the analysis published in our [paper](https://github.com/neherlab/pangraph#citing). - added `-K` option to the `build` command to control kmer length for mmseqs aligner, see this [commit](0857c36).
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In the
alignfunction (align.jl)@syncmacro on the loop in which threads are spawned.