Во-первых я ступил - while read -r line
Во-вторых, ну как бы не должно так быть:
$ cat file
$$4Vx----U062129.000,A,5555.5543,N,08888.0991,E,0.00,308,040212,,*01|0.8|133|2000|000D,0004|00FA0001983C0119|1D|00003D84~-
$$4Vx----U062231.000,A,5555.5543,N,08888.0991,E,0.00,308,040212,,*0B|0.9|133|2000|000E,0005|00FA0001983C0119|1D|00003D84--
$$4Vx----U062331.000,A,5555.5543,N,08888.0991,E,0.00,308,040212,,*0A|1.0|133|2000|0005,0005|00FA0001983C010F|1D|00003D84
yazu@kubuntu ~/tmp
$ cat file | while read -r line; do echo "$line"; done
$$4Vx----U062129.000,A,5555.5543,N,08888.0991,E,0.00,308,040212,,*01|0.8|133|2000|000D,0004|00FA0001983C0119|1D|00003D84~-
$$4Vx----U062231.000,A,5555.5543,N,08888.0991,E,0.00,308,040212,,*0B|0.9|133|2000|000E,0005|00FA0001983C0119|1D|00003D84--
$$4Vx----U062331.000,A,5555.5543,N,08888.0991,E,0.00,308,040212,,*0A|1.0|133|2000|0005,0005|00FA0001983C010F|1D|00003D84
То есть чудеса.