[BioC] vmatchPattern

[Richard Dannebaum [guest]]

When will vmatchPattern support indels?



 -- output of sessionInfo(): 

> reads[1:5]
  A DNAStringSet instance of length 5
    width seq
[1]    51 NTATTGGTAGCGAATTCCTGTACTGCTTCGACACACTGTACTCTTCAACTT
[2]    51 NCTTGGGATGCGAATTCCTGTACTGCTTCGCGGTGTCGTACTCTTCAACTT
[3]    51 NGAGGGTGTTCGAATTCCTGTACTGCTTCGAAATCTGGTACTCTTCAACTT
[4]    51 NTAGCGTTGACGAATTCCTGTACTGCTTCGCTCCACCGTACTCTTCAACTT
[5]    51 NCTGTTTGCCCGAATTCCTGTACTGCTTCGTACCGTTGTACTCTTCAACTT

> constant <- vmatchPattern("CGAATTCCTGTACTGCTTCG", reads[1:5], max.mismatch=1, with.indels=TRUE)

Error in .XStringSet.vmatchPattern(pattern, subject, max.mismatch, min.mismatch,  : 
  vmatchPattern() does not support indels yet

 

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