Dumpreads

dumpreads extracts reads from a bank and reports them in fasta or fastq format

 .USAGE.
   dumpreads  [options] <bank path>

 .DESCRIPTION.
   Takes an AMOS bank directory and dumps selected reads to
   stdout in FASTA or FASTQ format.

 .OPTIONS.
   -f            Dump reads in fastq format
   -Q int        Use this as the min base quality (default: 33 / Sanger FASTQ)
   -q            Dump qualities in fasta format instead of sequence
   -e            Use EIDs for FastA header instead of IIDs
   -r            Ignore clear range and dump entire sequence
   -c            Display clear range information on FASTA header for TIGR Assembler
   -E file       Dump just the eids listed in file
   -I file       Dump just the iids listed in file
   -L num        Set the maximum number of bases per line (Default: 70)
   -m num        Minimum IID to display (not included) (Default all; not compatible with -e,-E,-I options)
   -M num        Maximum IID to display (included) (Default all; not compatible with -e,-E,-I options)
   -h            Display help information
   -s            Disregard bank locks and write permissions (spy mode)
   -v            Display the compatible bank version
 
 .KEYWORDS.
   amos bank, reads, converters