After running cargo test:

running 10 tests test test_cli ... ok test test_help_exit_code ... ok test missing_reads ... ok test ont_amps_find_both_orientations ... FAILED test differentiate_artic_v3_from_vss ... FAILED test test_version ... ok test test_insufficient_arguments ... ok test non_matching_primer_sets ... ok test differentiate_vss_from_artic_v3 ... ok test differentiate_vss2_from_vss1a ... FAILED

failures:

---- ont_amps_find_both_orientations stdout ---- thread 'ont_amps_find_both_orientations' panicked at 'Unexpected stdout, failed fn(var) └── var as str:

command="/Users/mcampbell/Desktop/src/ampseer/target/debug/ampseer" "--primer-sets" "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/vss_18_28.bed.fasta" "--reads" "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/ont_vss_full_length_amp18rev_amp28for.fastq" code=1 stdout="" stderr="2022-01-25 17:12:39,767 ERROR [ampseer] Could not find reads at "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/ont_vss_full_length_amp18rev_amp28for.fastq"\nError: Invalid input\n" ', /rustc/db9d1b20bba1968c1ec1fc49616d4742c1725b4b/library/core/src/ops/function.rs:227:5 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

---- differentiate_artic_v3_from_vss stdout ---- thread 'differentiate_artic_v3_from_vss' panicked at 'Unexpected stdout, failed fn(var) └── var as str:

command="/Users/mcampbell/Desktop/src/ampseer/target/debug/ampseer" "--primer-sets" "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/primer_sets/ARTIC_v3.bed.fasta" "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/primer_sets/neb_vss1a.bed.fasta" "--reads" "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/artic_v3.fastq" code=1 stdout="" stderr="2022-01-25 17:12:39,767 ERROR [ampseer] Could not find reads at "/Users/mcampbell/Desktop/src/ampseer/tests/fixtures/artic_v3.fastq"\nError: Invalid input\n" ', /rustc/db9d1b20bba1968c1ec1fc49616d4742c1725b4b/library/core/src/ops/function.rs:227:5

---- differentiate_vss2_from_vss1a stdout ---- thread 'differentiate_vss2_from_vss1a' panicked at 'Unexpected stdout, failed fn(var) └── var as str: unknown

I'm sure my Rust on linux isn't up-to-date, but I got this:

error: failed to parse manifest at /mnt/home/mcampbell/src/ampseer/Cargo.toml

Caused by: feature edition2021 is required

this Cargo does not support nightly features, but if you switch to nightly channel you can add cargo-features = ["edition2021"] to enable this feature

This PR doesn't change the functionality of the code but rather makes some suggestions in line with Rust idioms. The biggest change is in populate_primer_count_hash where let key = if replaces the double-assignment of key and is_some is used at the insert step and then the rewrite of import_primer_sets to reduce use of mut and prefer a more "functional" style to a more "C-like" approach of initialising and then updating a hashmap.

Further down the code identify_primer_sets has an if-chain replaced with a match based on a clippy suggestion. I'm less sure that this is an improvement - it uses match rather than an if-chain, which is more ideomatic for Rust, but the use of Ordering::Equal etc might make things less readable to some users.

Hi!

This is a very nice tool.

Once you have enough confidence in it, it would be nice to create a package on bioconda to make it easier to integrate in workflow (e.g. I would like to add it to V-pipe, as we need primer autodetection for several components )

I can give a hand with that if needed.

nextera transposases cannot insert at the extreme ends of amplicons. To handle these libraries, it would be necessary to enable partial matches with expected start sequences.