Noteworthy changes in hichipper

Split .fastq files as input to HiC-Pro

As of version 0.5.3 of hichipper, users should be able to input split .fastq files into HiC-Pro and have hichipper function properly. No extra user flags are needed for this functionality. Thanks to our early users for helping us figure this out.

A note on duplicate PETs in loops

In certain versions (0.4.4 to 0.5.3) of hichipper, duplicates were not being filtered out by default. These duplicates were potentially inflating the number of PETs mapping to loops only.

In version 0.7.1, peaks are now called using all reads without again filtering duplicates as this is done during the HiC-Pro step.