Quote from Bob111:
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Long term losses can only offset long term gains.
Short term losses can only offset short term gains.--
i disagree. and so my tax preparation soft.
here is a simple solution for OP or anyone,who is in doubt-grab an old tax preparation app CD like a turbo tax or tax cut or whatever. they are free(cause it's useless) and create a dummy return. insert whatever numbers you want to play with. check results
At least in 2012 long term and short term were separated. Maybe it's changed in 2013.
http://www.irs.gov/pub/irs-prior/i1040sd--2012.pdf
Could you explain the output from your software because the pdf above is pretty clear about the separation.