SAM format: single vs multiple hits

[darked89]

According to the specification, there is SAM flag:
0x0100 0x0100 "the alignment is not primary (a read having split hits may have multiple primary alignment records)"

but using http://picard.sourceforge.net/explain-flags.html I could not find it i.e in Tophat SAM output file.

My problem is a follows: given that a query sequences were mapped without splits, how can I distinguish between these having just one hit in the genome (SH) and these with multiple hits?

[sterding]

I made a learning note for SAM format, which might be helpful to your question:

http://onetipperday.blogspot.com/2012/07/deeply-understanding-sam-tags.html