There are two special circumstances that may apply once you have your data. They are dealing with "carry over positions" and handling stock splits.
The carryover position issue arises when a trader has positions that remained open at the end of the previous trading year but were closed during the year at issue such that the gain or loss should be included. In order, to calculate the gain or loss, the data file must be adjusted to include the trade opening information from the prior year. More detailed information about how to do this is provided in Appendix C. If this is not your first year using the TradeMatcher software then last year's results will have the carryover information. Otherwise, you will need to review your older brokerage data to glean the position opening information.
The second issue that might arise would occur in the event of a stock split. If there is a stock split during the period while a position is held, the opening number of shares must be manually adjusted to match the number of shares after the split. A failure to adjust the opening position will result in an inaccurate matching and part of the shares will show in the file that indicates a position is still open (even though it wasn't). If you had a stock split you can ordinarily find details online for the security if you can't tell from your data the nature of the split. Simply adjust the number of shares in the input data and run the tradematcher again with the new data.
By way of quick example, if you purchased 100 shares of INTC which split 2 for 1 while you were holding it, you would simply adjust the number of purchased shares from 100 to 200 so that the closing shares will be properly apportioned against the opening shares. If you fail to do so, you would notice in the stillopen.csv file that you are shown still holding 100 shares of INTC short when in fact you are not actually! This is the tipoff that you had a split issue you may have forgotten to adjust!