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.