nebiolabs / mark-nonconverted-reads Goto Github PK

to preserve what was done to a file, we should write an appropriate @pg line.

Thanks for the handy tool. Just wanted to flag something, which I noticed today. Haven't fully verified this, but I think there's a bug in the soft-clipping step. For instance, let's say you have a read which is soft-clipped at the beginning. Then when you grab coords = read.get_reference_positions(full_length = True), you get leading Nones. The coords = softclip(coords) removes the Nones from the coords but not from the read.query_sequence. This means that coords.index(coord) no longer refers to the right base in the read sequence.

Let me know if I'm making a dumb mistake, which I probably am. Once I verify I will open a PR, which will probably just involve editing the softclip function to subset the read.query_sequence with the same bounds.

Let's add this to bioconda - that will make it easier to distribute (both internally and externally)

This tool is a bit too slow for routine use.
Any ideas about how to speed it up?

with the filter jobs:

without: