Reads in an extended BED tag alignment file. An example line given below:
49 . U1 . 1 . . 23 chr2 -234567
The line above specifies a 23-bp portion of the tag tag with id 49 was
aligned with 1 mismatch to the negative strand of chr2 at position 234567.
read.meland.tags(filename, read.tag.names = F, fix.chromosome.names = T)name of the extended BED file
whether to read in tag names
whether to remove ".fa" from the sequence name ends.
A vector of 5' tag coordinates, with negative values corresponding to tags mapped to the negative strand.
Quality expressed as a float x.y, where x is tag.length - aligned.tag.portion.length, and y is the number of mismatches (must be less than 10).
Tag names, if read.tag.names was set