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bioinfologics / satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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gff3 files are not zero-based #1

Closed jjdevega closed 8 years ago

jjdevega commented 8 years ago

~ SatsumaToGFF -i satsuma_summary.chained.out | sort -k1,1 -k3,3 | head -n 1 scaffold_1 Satsuma block 0 339 - . ID=sblock_1850;Name=sblock_1850;Target=Chr01

But gff3 files are one-based in the specs, so the first base should be 1, not 0. For info about zero-based and one-based formats in bioinformatics: https://www.biostars.org/p/84686/

In fact, if you try to manipulate that file, it gives error downstream (as expected). Eg. ~ SatsumaToGFF -i satsuma_summary.chained.out | sort -k1,1 -k3,3 | head -n 1 | bedtools sort -i - Error: malformed GFF entry at line 1. Start was greater than end. Exiting.

jonwright99 commented 8 years ago

I've pushed an update to fix this. You will need to get the latest version of the code and recompile.