Merge meta

[SaberHQ]

Dear Chen, Thanks for the great work on this pull request. I have several suggestions and comments before you can merge this branch. Please let me know if you have any questions.

I tested the "metagenome" mode with different scenarios and parameter sets and everything worked well, except for one error run. The simulation code crashed when I asked for "perfect" reads. It produced "local variable referenced before assignment" runtime error. Please take a look into this before merging this branch into master.

Below, you can find some comments as well.

• Please update the README file to reflect the latest changes to the read_analysis/simulation argument parser codes.
• It would be great to add more information regarding the KmerBias parameter in the argument parser help file. For example, it would be helpful to provide a suggested range of numbers one can pass to the -k parameter.
• As for the abundance config file, I believe the description is a bit confusing. It says “the abundance for each sample need to sum up to 100.” Perhaps we can change it to “Abundance of all samples need to sum up to 100”.
• In the "genome" and "transcriptome" modes, we used to have the -n parameter which controls the total number of synthetic reads the user want to simulate. I do see that you implemented this option within the abundance config file. However, I believe that we should provide more clarification of this in the README file and help function. In addition, I think the header line is a bit hard to understand and I suggest using some different numbers to avoid any confusion.
• I do suggest to update the "Publications" section of the README file to clarify which manuscript to use and cite for each purpose.

[cheny19]

Hi @SaberHQ , thanks for such thorough review. I have merged the branch and will revise the code and README accordingly.