Cole Lyman issues

Results 12 issues of


                                            Cole Lyman

Paired read processing

The algorithm runs the unit tests successfully now, I imagine that it needs to be integrated into the core so that the newly aligned reads are actually used, right? If...

Intersection fix

Hey Guillaume, I noticed that the return array from the `intersection_uint32` method always had a size of 0, and after inspecting the code I saw why. From what I understand...

Rename the specific SSE 4.2 popcnt calls

Hey Guillaume, After trying to compile with a compiler that didn't have SSE 4.2 enabled, I discovered that the following changes would allow the code to work on non-SSE enable...

Move read filtering to after merging in CRISPResso

* Move read filtering to after merging This is in an effort to be consistent with the behavior and results of CRISPRessoPooled. * Properly assign the correct file names for...

Get custom Needleman Wunsch alignment matrix location

@kclem is there a particular reason why this alignment matrix can't be customized?

Add nitem (numbered lists)

I have found this useful in my slides so I thought that it may be useful upstream. I have essentially copied the implementation for `item` and replaced the bullet with...

Failed assert in stream_encoding.h:152

I have encountered this failed assertion (`assert(currBit / 8 < output.size());`, [stream_encoding.h:152](https://github.com/jts/dbgfm/blob/master/stream_encoding.h#L152)) when loading a genome. It happens with the [Drosophila melanogaster genome (FASTA download link)](http://bit.ly/2wbFrZc). I have inspected the...

Cole Lyman