Mikko Rautiainen
Mikko Rautiainen
- Non-GAM textual output (GAF?) to simplify downstream processing of alignments This sounds totally reasonable. - Independent aligner library (to embed in other tools) I'd like to do this as...
The current version does not use the embedded paths.
There is no option but if you have `alns.gaf` and `reads.fa` then you can find the unmapped reads with: ``` cut -f 1 < alns.gaf | uniq | cat -
The errors look like GraphAligner bugs. Those reads will not have alignments in the output but other reads will not be affected. Could you please upload the graph and the...
The environment file was generated by conda export which apparently is machine specific then. You can try to have conda figure out the dependencies into your environment with: `conda install...
1. Yes, this should be possible. jemalloc was the fastest option based on evaluations a couple of years ago but this might have changed since then. 2. Could be 3....
Hi, GraphAligner can't find any sequences in the input file (`Input reads: 0 (0bp)` in the output). Could you please double check that the input file is a fasta or...
> It seems that if the input file is called "a", then no sequences are read in. However, if it is called "a.fasta" then sequences are read. This is because...
It's supposed to support vg graph. Could you please upload the graph?
This seems to be caused by changes in the vg file format. Up until vg version 1.40.0 the default was the protobuf format which GraphAligner can read, and then it...