fastqSample

usage: fastqSample [opts]
  Input Specification
    -I NAME  input name (prefix) of the reads
    -T T     total number of mate pairs in the input (if not supplied, will be counted)
    -L L     length of a single read (if not supplied, will be determined)
    -U       reads are unmated, expected in *.u.fastq

  Output Specification
    -O NAME  output name (prefix) of the reads (default is same as -I)
    -A       automatically include coverage or number of reads in the output name
    -m L     ignore reads shorter than L bases
    -max     don't sample randomly, pick the longest reads

  Method 1: specify desired output coverage:
    -g G     genome size
    -c C     desired coverage in the output reads

  Method 2: specify desired number of output pairs
    -p N     for mated reads, output 2N reads, or N pairs of reads
             for unmated reads, output N reads

  Method 3: specify a desired fraction of the input:
    -f F     output F * T pairs of reads (T as above in -t option)
             0.0 < F <= 1.0

  Method 4: specify a desired total length
    -b B     output reads/pairs until B bases is exceeded


Samples reads from paired Illumina reads NAME.1.fastq and NAME.2.fastq and outputs:
    NAME.Cx.1.fastq and N.Cx.2.fastq (for coverage based sampling)
    NAME.n=N.1.fastq and N.n=N.2.fastq (for coverage based sampling)

If -T is not supplied, the number of reads will be counted for you.

ERROR: no name supplied with -I.
ERROR: no method supplied with -c, -p, -f or -b