Update CRISPRessoPooledCORE.py

Fix debug statement

Create html report for CRISPRessoComparePooledWGS

Update test results for more flexible pooled alignment

The relaxing of bowtie parameters allowed more reads to align, which changed the expected test results for CRISPRessoPooled

HDR Updates - yw #82

Multiple amplicon names are resolved before adding the HDR amplicon -- unnamed amplicons are named Amplicon{i} for each amplicon.
Plot 4g data (nuc pct table, mod pct table for all reads aligned to the first reference) is output and linked to from the plot display
Ambiguous reads don't contribute to plot 4g data (which would otherwise lead to double counting and pct values > 1)

Update README.md

Fix plot window cloning from Ref1 to HDR

Plot window for sgRNA will be the same length after cloning even if the window is shorter or longer after comparing between ref1 and HDR.

Update histogram x-limits, caption, and data

Version bump to v2.0.42

Fix bug in read counting for interleaved fastqs

Prime editing updates

prime editing guides are shown as input on report output
file names are produced without spaces