It would be nice to add the -q flag as it appears in trim-low-abund.py to interleave-reads.py and extract-paired-reads.py. I feel like it is taking a lot of energy (for lack of a better word) to write to stdout for some larger files-- especially when passing these through snakemake or the like.
It looks like it might be as simple as adding a few lines to each of the scripts. I started a separate branch -- but I am not sure if my solution is quite right.
It would be nice to add the
-qflag as it appears intrim-low-abund.pytointerleave-reads.pyandextract-paired-reads.py. I feel like it is taking a lot of energy (for lack of a better word) to write to stdout for some larger files-- especially when passing these through snakemake or the like.It looks like it might be as simple as adding a few lines to each of the scripts. I started a separate branch -- but I am not sure if my solution is quite right.