I am mapping my reads using smalt (for specific reasons) program and I am wondering if any one have come across smalt's sam output formatting options? you can specify format output with -f flag. it also has some extensions i.e
where x is for cigar string, nohead is for no headers and clip is for hard clipping. I think smalt by default hard clip reads. its not mentioned anywhere what to use in case I dont want hard clipping? I tried values like no clip etc...but it doesnot work. Any ideas?