esteinig / nanoq

Minimal but speedy quality control for nanopore reads in Rust :bear:

MIT License

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Report outputs #32

Closed esteinig closed 2 years ago

esteinig commented 2 years ago

--stats/-s now outputs the summary to stdout --> #31

nanoq -i test.fq -s > report.txt

--report/-r always writes the report to a file

nanoq -i test.fq -s -r report.txt

report is not output to stderr when filtering (or ever); use explicit report file option

nanoq -i test.fq -r report.txt > reads.fq

--json/-j outputs the report in JSON (equivalent to -vvv) --> #30

codecov-commenter commented 2 years ago

Codecov Report

Merging #32 (58d6546) into master (b78c338) will not change coverage. The diff coverage is 100.00%.

@@            Coverage Diff            @@
##            master       #32   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files            4         4           
  Lines          463       557   +94     
=========================================
+ Hits           463       557   +94

Impacted Files	Coverage Δ
src/cli.rs	`100.00% <ø> (ø)`
src/needlecast.rs	`100.00% <ø> (ø)`
src/utils.rs	`100.00% <100.00%> (ø)`

esteinig commented 2 years ago

@mbhall88 @kaiseriskera

How is this looking?

esteinig commented 2 years ago

fixed JSON string output

esteinig commented 2 years ago

removed stderr report output entirely (see first comment, edited)