[BUG] Different reads have the same read numbder

[YuanlongLiu]

In the .singlePrepUMI4C function, the new_id_R2, new_id_R1 are computed from 'seq_len(length(filtered_reads_fqR1))', which can duplicate for different iterations of the 'repeat' function, i.e, different reads will get the same read number

This new_id_xx is used later on in 'gr_sp <- GenomicRanges::GRangesList(GenomicRanges::split(gr, gr$readID))'. I have the feeling that this will cause problem

[mireia-bioinfo]

Thanks for repporting this! It has been fixed in the latest commit.

[YuanlongLiu]

Hi, it should be:

new_id_R1 <- paste0(umis, ":", "UMI4C:", filtered_reads + seq(1, length(filtered_reads_fqR1)), ":R1")

not

new_id_R1 <- paste0(umis, ":", "UMI4C:", seq(filtered_reads + 1, length(filtered_reads_fqR1)), ":R1")