Added code to handle snps less than 30nt from start/end of chromosomes#2
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ethering wants to merge 1 commit intogersteinlab:masterfrom
Open
Added code to handle snps less than 30nt from start/end of chromosomes#2ethering wants to merge 1 commit intogersteinlab:masterfrom
ethering wants to merge 1 commit intogersteinlab:masterfrom
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Hi,
We're applying FunSeq2 to non-human organisms, which have quite fragmented assemblies. FunSeq was throwing errors when if found a variant either within 30 nts of the start or end of a scaffold. As human chromosomes have long stretches of Ns at the start/end, this wouldn't be a problem, but it was for us so I've added some code that makes a hash of chromosome/scaffold lengths and alters the co-ordinates for the variants found near the start or end of each chromosome/scaffold.
Hope you find it helpful.
Best wishes,
Graham Etherington