Given a BAM file, several regions are sampled depending on the size of the genome and number of processors to estimate the paired-end fragment length. Properly paired reads are preferred for computation.

usage: bamPEFragmentSize [-h] [--histogram FILE] [--numberOfProcessors INT]
                         [--plotTitle PLOTTITLE] [--verbose] [--version]
Positional arguments:
bam BAM file to process
optional arguments
--histogram, -hist
 Save a .png file with a histogram of the fragment length distribution.
--numberOfProcessors=1, -p=1
 Number of processors to use. The default is to use 1.
--plotTitle=, -T=
 Title of the plot, to be printed on top of the generated image. Leave blank for no title.
 Set if processing data messages are wanted.
--version show program’s version number and exit