Primers

**Full Changelog**: https://github.com/Lattice-Automation/primers/compare/v0.5.3...v0.5.4

- fix: `primers score` works if the amplification is across the zero-index

**Full Changelog**: https://github.com/Lattice-Automation/primers/compare/v0.5.0...v0.5.3

- `primers score SEQ1 SEQ2 -s TEMPLATE_SEQ` now returns separate `tm` and `tm_total`s. This affects score:


$ primers score GGTCTCAATGAGACAATA AAAAAATTTCGTATGCTGACCTAG -s AATGAGACAATAGCACACACAGCTAGGTCAGCATACGAAA --json | jq
[
{
"seq": "GGTCTCAATGAGACAATA",
"len": 18,
"tm": 39.4,
"tm_total": 55,
"gc": 0.4,
"dg": -1.86,
"fwd": true,
"off_target_count": 0,
"scoring": {
"penalty": 49.9,
"penalty_tm": 22.6,
"penalty_tm_diff": 19.6,
"penalty_gc": 2,
"penalty_len": 2,
"penalty_dg": 3.7,
"penalty_off_target": 0
}
},
{
"seq": "AAAAAATTTCGTATGCTGACCTAG",
"len": 24,
"tm": 59,
"tm_total": 61.6,
"gc": 0.4,
"dg": 0,
"fwd": false,
"off_target_count": 0,
"scoring": {
"penalty": 25.6,
"penalty_tm": 3,
"penalty_tm_diff": 19.6,
"penalty_gc": 2,
"penalty_len": 1,
"penalty_dg": 0,
"penalty_off_target": 0
}
}
]

**Full Changelog**: https://github.com/Lattice-Automation/primers/compare/v0.4.0...v0.5.0

- breaking change: creating primers command moved into `primers create` from just `primers`
- add: `primers score` sub-command to score primers (https://github.com/Lattice-Automation/primers/issues/4):


$ primers score --json GGTCTCAATGAGACAATAGCACACAC GAAGACTTTCGTATGCTGACCTAG | jq
[
{
"seq": "GGTCTCAATGAGACAATAGCACACAC",
"len": 26,
"tm": 67,
"tm_total": 67,
"gc": 0.5,
"dg": -1.86,
"fwd": true,
"off_target_count": 0,
"scoring": {
"penalty": 13.23,
"penalty_tm": 5,
"penalty_tm_diff": 2.5,
"penalty_gc": 0,
"penalty_len": 2,
"penalty_dg": 3.73,
"penalty_off_target": 0
}
},
{
"seq": "GAAGACTTTCGTATGCTGACCTAG",
"len": 24,
"tm": 64.5,
"tm_total": 64.5,
"gc": 0.5,
"dg": 0,
"fwd": false,
"off_target_count": 0,
"scoring": {
"penalty": 6,
"penalty_tm": 2.5,
"penalty_tm_diff": 2.5,
"penalty_gc": 0,
"penalty_len": 1,
"penalty_dg": 0,
"penalty_off_target": 0
}
}
]

**Full Changelog**: https://github.com/Lattice-Automation/primers/compare/v0.3.2...v0.4.0


primers create -r GGTCTC -j $SEQ | jq
[
{
"seq": "CTACTAATAGCACACACGGG",
"len": 20,
"tm": 63.6,
"tm_total": 63.6,
"gc": 0.5,
"dg": 0,
"fwd": true,
"off_target_count": 0,
"scoring": {
"penalty": 2.6,
"penalty_tm": 1.6,
"penalty_tm_diff": 0,
"penalty_gc": 0,
"penalty_len": 1,
"penalty_dg": 0,
"penalty_off_target": 0
}
},
...

**Full Changelog**: https://github.com/Lattice-Automation/primers/commits/v0.3.3

- rename parameters, `opt_` -> `optimal_`