Usage:
   sam-dump [options] path[ path ...]

Options:
  -s|--seqid                       print reference SEQ_ID in RNAME instead of 
                                   NAME 
  -u|--unaligned                   output unaligned reads 
  -c|--cigar-long                  output long version of CIGAR 
  -r|--header                      always reconstruct header 
  --aligned-region <name[:from-to]>  Filter by position on genome. Name can 
                                   either be file specific name (ex: "chr1" or 
                                   "1"). "from" and "to" are 1-based coordinates 
  --matepair-distance <from-to|unknown>  Filter by distance beiween matepairs. 
                                   Use "unknown" to find matepairs split 
                                   between the references. Use from-to to limit 
                                   matepair distance on the same reference 
  -=|--hide-identical              Output '=' if base is identical to reference 
  --gzip                           Compress output using gzip 
  --bzip2                          Compress output using bzip2 
  -g|--spot-group                  Add .SPOT_GROUP to QNAME 
  -n|--no-header                   Do not output headers 
  --fastq                          Produce Fasta formatted ouput 
  --fasta                          Produce FastQ formatted ouput 
  -p|--prefix <prefix>             Prefix QNAME: prefix.QNAME 

  -h|--help                        Output brief explantion for the program. 
  -V|--version                     Display the version of the program then 
                                   quit. 
  -L|--log-level <level>           Logging level as number or enum string. One 
                                   of (fatal|sys|int|err|warn|info) or (0-5) 
                                   Current/default is warn 
  -v|--verbose                     Increase the verbosity level of the program. 
                                   Use multiple times for more verbosity.