If the file(s) in question contain no 0x0a (line-feed) characters, then just change 0x0d (carriage-return) to line-feed "temporarily" to make your normal line-oriented processing easier, then change it back:

perl -pe 'tr/\x0d/\x0a/' source.file | easy_line_filter | perl -pe 'tr
+/\x0a/\x0d/' > edited.source.file
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