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Hard to say without data, or code being used (to know input processor). Should not be due to duplicate lines (which are fine). Theoretically could have something to do with differences in linefeed detection -- java-merge-sort accepts all three (\n, \r and \r\n; windows and macos use different ones), not sure if wc does.
$ wc -l ngram.data; wc -l ngram_sort.data 10069731 ngram.data 10067458 ngram_sort.data
after sorting, I lost about 2273 lines? why?
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