autogenerate index for other native types

GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

http://genomearchitect.readthedocs.io/

Other

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Open nathandunn opened 5 years ago

nathandunn commented 5 years ago

[ ] GFF3Tabix (sort using a simplified grep) and then tabix. Something like:
- (grep ^"#" in.gff3; grep -v ^"#" in.gff3 | sort -k1,1 -k4,4n) > out.sorted.gff3 or gt gff3 -sortlines input.gff > output.gff
- bgzip out.sorted.gff3
- tabix -p out.sorted.gff3.gz
- all should be available in htjsdk or the native JVM
[ ] BAM
[ ] VCF

nathandunn commented 5 years ago

Would need to find a way to sort these first in a semi-low-memory that can be a longish-job.