Circ

[madagiurgiu25]

Hi,

I wanted to simulate reads using pbsim2, but on a circular genome. Thus, I thought could be a useful feature for your package.
For this, I adapted the template to be circular and choose mersenne_twister_engine as random number generator to sample uniformly the start of the read (offset).

Best,
Mădălina

[madagiurgiu25]

@yukiteruono , I have merged the feature into the master branch. The code builds successfully (see --circular option):

./src/pbsim 

USAGE: pbsim [options] <reference>

 <reference>           FASTA format file (text file only).

 [general options]

  --prefix             prefix of output files (sd).
  --id-prefix          prefix of read ID (S).
  --depth              depth of coverage (20.0).

 ...

 [options of model-based simulation].

  --hmm_model          HMM model of quality code.
  --length-mean        mean of length model (9000.0).
  --length-sd          standard deviation of length model (7000.0).
  --accuracy-mean      mean of accuracy model (0.85).
  --circular           circular genome (0).
                       to enable this use 1.