[Samtools-help] Get reads count from SAM file

[<rob...@no...>]

Dear All,

I need to get the total read counts which are mapped to the reference 
genome from SAM file.  Which field from the SAM file will give such 
information.
Information that I need to get as list here:
1)  Total read counts with 0 mismatch, 1 mismatch, and 2 mismatch from SAM 
file
2)  Total unique read counts from SAM file are mapped the reference 
genome.
3) Any software tool or Unix command can parse the information out the SAM 
file

Thanks
Robin
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