All pull requests

Pull requests

• Add --max-shared-kmer-pvalue: chance-based minimum shared k-mers, measured on Swiss-Prot

  #161·olgabot opened Oct 31, 2026Contributor·

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  7

• Name protein ID lists and the k-mer-to-protein index plainly

  #160·olgabot opened Oct 30, 2026Contributor·

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  2

• Read the inverted index in place from posting files (Swiss-Prot search 165 s to 1 s)

  #159·olgabot opened Oct 21, 2026Contributor·

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  12

• Count Pr(same class) from each region, so low-complexity regions get honest E-values

  #157·olgabot opened Oct 20, 2026Contributor·

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  8

• Add massspec18: the 20 residues with I=L and Q=K merged, for mass-spec peptides

  #156·olgabot opened Oct 20, 2026Contributor·

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  9

• Build the "expected one of" alphabet lists from Alphabet::all()

  #155·olgabot opened Oct 19, 2026Contributor·

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  1

• Count Karlin-Altschul fit regions per score bin as they are found

  #154·olgabot opened Oct 17, 2026Contributor·

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  29

• Skip a query's identical database entry in every search, and test it

  #153·olgabot opened Oct 16, 2026Contributor·

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  28

• Key index entries by their sequence, not their k-mer set

  #152·olgabot opened Oct 16, 2026Contributor·

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  53

• Draw the three cysteine-aware readings of two toxins that share a framework

  #150·olgabot opened Oct 16, 2026Contributor·3/3·

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  9

• PR template: Olga's Why and What I learned, checked before merge

  #149·olgabot opened Oct 15, 2026Contributor·

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  17

• Add hp_pbotc_1st_ed_hpc3 (cys_hp3), and let a cys2 index be searched

  #148·olgabot opened Oct 14, 2026Contributor·2/3·

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  29

• Add the cys2 alphabet on the v0.4.0 release

  #147·olgabot opened Oct 14, 2026Contributor·

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  15

• Add aro_hyd_chg_pol4 and aro_hyd_arg_chg_pol5 (sticker and spacer alphabets)

  #146·olgabot opened Oct 14, 2026Contributor·

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  12

• Add the cys2 alphabet: cysteine against every other residue

  #145·olgabot opened Oct 14, 2026Contributor·1/3·

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  22

• search: --ka-r-database, to search with a fit made on another index

  #144·olgabot opened Oct 13, 2026Contributor·

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  26

• Skills: rules from Olga's review comments, Oct 5-11

  #143·olgabot opened Oct 13, 2026Contributor·

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  24

• Search report: draw rows with no run, --min-runs to leave them out, dot plot labels that fit

  #142·olgabot opened Oct 13, 2026Contributor·

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  22

• Key index entries by their sequence, so a target's hits carry its own coordinates

  #141·olgabot opened Oct 10, 2026Contributor·

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  10

• Remove two unused ProteomeIndex fields; fail CI on dead_code allows

  #137·olgabot opened Oct 6, 2026Contributor·

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  30

• Test the run E-value on random sequences and on dipeptide-shuffled decoys

  #134·olgabot opened Oct 3, 2026Contributor·

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  12

• Give every row a run E-value, and drop the Poisson E-value

  #133·olgabot opened Oct 3, 2026Contributor·

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  51

• Add the mid-p run E-value, and score the decoy test on other proteins' shuffles

  #130·olgabot opened Oct 1, 2026Contributor·

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  31

• Extend matched regions by default when the index holds a fit

  #114·olgabot opened Sep 30, 2026Contributor·

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  28

• Extend regions when there is no Karlin-Altschul fit, instead of refusing the search

  #113·olgabot opened Sep 30, 2026Contributor·

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  4