Performs and outputs various statistical tests for each contig in a GSS basepile output. it is assumed that the information for each contig is 1000 bases long. The following statistics are outputted in a tab-delimitated list for each contig by the script:

  • Reference Match Length: The index of the last known base (i.e. not 'N')
  • Target Match Sum: The number of known bases (i.e. not 'N')
  • Coverage Proportion: proportion of 'Target match sum' to ' Reference match length'
  • Average Density: The average density value for all bases within ' Reference match length'
  • Median Density: median density of the entire range of density values

python BPstats.py