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Old 10-16-2011, 09:11 PM   #5
Location: Seattle

Join Date: Jul 2011
Posts: 98

Originally Posted by cedance View Post
I remember vaguely but there is a --format=sam parameter to specifically output the results in SAM format. You should check out the parameter list and add it to your command line options accordingly.
Thanks so much, cedance. I see that that is one of my critical mistakes. I thought I had read through the options carefully, but I guess I hadn't read them carefully enough. I very much appreciate the help.

Best wishes,

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