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ShixiangWang / sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
https://shixiangwang.github.io/sigminer/
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getSeq #422

Closed ShixiangWang closed 1 year ago

ShixiangWang commented 1 year ago
image 
  ss <- BSgenome::getSeq(
    x = ref_genome,
    names = extract.tbl$Chromosome,
    start = pmax(extract.tbl$Start - 2, 1L),
    end = extract.tbl$End + 2,
    as.character = TRUE
  )

Browse[2]> BSgenome::getSeq(ref_genome, "chr20", start = 63311965, end = 63311969)
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord,  : 
  solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start (63311965) is > refwidth + 1
ShixiangWang commented 1 year ago

这种情况一般不发生，相关问题也木有后续，以后再考虑吧。