Stdin/stdout seem to be not quite right when input is piped in #7
Description
My recent round of testing showed that when using a pipe to supply input to bcgt.py the output does not look right (on the screen) even if the results going into the file end up being correct. I suspect there is some kind of interaction going on with file io. Perhaps I need to make sure a buffer is flushed or something like that? Not sure yet. Will investigate this further, but since it is not giving errors in the resulting file I'm not going to worry as much about this as I would if I were seeing wrong results.