Reads in MAQ alignment results in text format (that results from "maq mapview" command.)
read.maqmap.tags(filename, read.tag.names = F, fix.chromosome.names = T)MAQ text output file
Whether the tag names should be read in
Whether to remove ".fa" from the end of the sequence names
A vector of 5' tag coordinates, with negative values corresponding to tags mapped to the negative strand.
Number of mismatches
Tag names, if read.tag.names was set