Implement Guard Rails

[Colelyman]

The goal of the guard rails is to provide users with informative warnings when their analysis could potentially be compromised. We want to create a system where we can have multiple guard rails for different conditions. These warning should be displayed at the end of the shell output as well as in the report so that they are readily apparent.

Some thought should be taken as to how we implement the guard rails. We could have a class for each guard rail that inherits from a parent guard rail class that handles the display of the warning message. I'm open to other ideas on how to implement this.

We should add a new section to the crispresso2_info['run_data'] object to hold all of the guard rail messages. This will make it easy to display the messages in report.

Guard Rails

Here are some guard rails that we can implement first.

• [x] Low number of total reads (< 10000)
• [x] Low number of overall reads aligned (< 90%)
• [x] Low number of reads aligned to an amplicon
• [x] High number of reads aligned to another amplicon
• [x] High number/percent of deletions/indels outside of quantification window (which could mean the wrong guide therefore incorrect quantification)
• [x] Low alignment rates at either end of the amplicon (which could mean the wrong PCR primers)
• [x] High rates of substitutions globally (which could mean poor sequencing quality
• [x] Short guides (< 19) or amplicons (< 50)
• [x] When using paired sequences, many reads fail to merge (which could mean too short read length or incorrect primers). Note: let's wait to implement this until Fastp is merged in https://github.com/pinellolab/CRISPResso2/pull/253.
• [x] Many reads fail basepair quality filters. Note: let's also wait for Fastp with this one.

[Colelyman]

It would be great to style the guard rails using the Bootstrap alert class at the top of the report.

<div class="alert alert-danger" role="alert">
  This is a danger alert—check it out!
</div>

Source: https://getbootstrap.com/docs/4.0/components/alerts/