sam_utils.py problem

[obenno]

Hi,

Thanks for the amazing tool. I found a little problem in misopy/sam_utils.py. https://github.com/yarden/MISO/blob/1ca049faa6f122751db25e8be49f04a695260557/misopy/sam_utils.py#L254

If the input bam includes secondary alignment (which is default for many mapping tools), the len(read) will has a value larger than 2, yet they were not unpaired, might be properly paired. In the subsequent code they will be discarded, despite whether their first alignment is good.

https://github.com/yarden/MISO/blob/1ca049faa6f122751db25e8be49f04a695260557/misopy/sam_utils.py#L281 It seems that should be %(len(to_delete)-num_unpaired)

Could you please make the function compatible to bam with secondary alignment or state that secondary alignment should be removed in MISO documentation? Thanks.

Regards, obenno