Usage: sra-pileup <path> [options] Options: -r|--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 -q|--minmapq <min. mapq> Minimum mapq-value, alignments with lower mapq will be ignored (default=0) -o|--outfile <output-file> Output will be written to this file instead of std-out -t|--table <table> What table to use (p/s/e) p..primary alignments, s..secondary alignments e..evidence alignments (default=p) -d|--duplicates <duplicates> Don't ignore dups (0/1) -m|--mode <output-modes> Output-format: 0...samtools, 1...just counters (default=0) -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. --report <type> Control program execution environment report generation (if implemented). One of (never|error|always). Default is error