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esteinig / nanoq

Minimal but speedy quality control for nanopore reads in Rust :bear:
MIT License
109 stars 9 forks source link

Basic summary statistics #3

Closed esteinig closed 2 years ago

esteinig commented 4 years ago

Besides filtering by read length and average quality nanoq now outputs some summary statistics similar to NanoStat as simple numerics to STDERR:

29082396 5000 62483 120 5816 2898 11.87 12.02

corresponding to: 

bp_total num_reads longest_reads shortest_read mean_length median_length mean_q median_q
esteinig commented 4 years ago

Run the command line interface with default flags (--length 0, --quality 0) to skip filters and to compute only statistics:

nanoq -f test.fq
mbhall88 commented 2 years ago

It would be nice to add an option -H,--header maybe that outputs the corresponding headers for the stats? I regularly have to come back to the webpage to look up which is which. Or maybe you could even add it in the long help menu for the stats option?

esteinig commented 2 years ago

Good point! I'll fix something up over the weekend. Do you think hardcoding headers into the output would be too much? Or more convenient?

mbhall88 commented 2 years ago

Up to you mate. Leave them out by default I reckon, that way there are no compatibility problems. Then as I said, add an option to output them?

esteinig commented 2 years ago

Sounds like a good solution, thanks for your input!