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.