v0.5.4

Full Changelog: v0.5.3...v0.5.4

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

v0.5.3

Full Changelog: v0.5.0...v0.5.3

• primers score SEQ1 SEQ2 -s TEMPLATE_SEQ now returns separate tm and tm_totals. 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
    }
  }
]

v0.5.0

Full Changelog: 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 (#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
    }
  }
]

v0.4.0

Full Changelog: 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
    }
  },
...

v0.3.3

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

• rename parameters, opt_ -> optimal_