The reason for is is DOS to use CRLF (carriage return + line feed) for line endings while unix uses LF (line feed) only.
If only few files need to be changed, vi/vim is the tool of choice.
After opening up the file, enter command mode to run this macro:
To get the ^M do not actually enter it as is. Insert it by typing the CTRL-V CTRL-M sequence instead.
Not as eloquent, but does the job.