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smarco / gem3-mapper

GEM-Mapper v3
GNU General Public License v3.0
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chromosome names #19

Closed igordot closed 4 years ago

igordot commented 4 years ago

I am using the SourceForge binaries, since it seems gem-mappability is not available in the GitHub version. I tried to index a genome with contigs like:

>chr1  AC:CM000663.2  gi:568336023  LN:248956422  rl:Chromosome  M5:6aef897c3d6ff0c78aff06ac189178dd  AS:GRCh38

The old indexer parses those contig names as chr1 AC (not chr1). Is there a way to resolve that?

smarco commented 4 years ago

This repository is for the latest release of the gem-mapper (GEMv3). If you have any issue with the old binaries (GEMv2) don't hesitate to contact the developers by email (Paolo Ribeca paolo.ribeca@gmail.com and Santiago Marco Sola santiagomsola@gmail.com).

In this case, the old GEMv2 parses the whole line and there is no option to do otherwise. The easiest solution is to adapt the input mFASTA to remove trailing tags on the sequence name (i.e., leave ">chr1" and remove the rest).

Sorry for the inconvenience,