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aerial.bio.utils.filters
Various scoring, filtering, of sequence data.
Various scoring, filtering, of sequence data.
percent-pass-qscoreclj
(percent-pass-qscore qc qc-ctpt)For qc line qc, return % qc > qc-ctpt value
For qc line qc, return % qc > qc-ctpt value
phred-scoresclj
Sangor format Phred score encoding/decoding map. Sangor format encodes Phred scores from 0-93 as ASCII using offset 33 (ASCII character codes 33-126). NOTE, as of end Feb 2011 all Illumina sequencing produces fastqs with this format.
Sangor format Phred score encoding/decoding map. Sangor format encodes Phred scores from 0-93 as ASCII using offset 33 (ASCII character codes 33-126). NOTE, as of end Feb 2011 all Illumina sequencing produces fastqs with this format.
prob-correct->phred-scoreclj
(prob-correct->phred-score p)Convert a probability p of a base being correct to corresponding Phred score. Note that the std mapping (definition of phred score) is a mapping from the probability -p of a base being _in_correct.
Convert a probability p of a base being _correct_ to corresponding Phred score. Note that the std mapping (definition of phred score) is a mapping from the probability -p of a base being _in_correct.
qcscore-min-entropyclj
(qcscore-min-entropy base% info% winsize)Compute minimum entropy for a distribution of kmers of size winsize over an msg with 'infinite' non repeated alphabet.
Compute minimum entropy for a distribution of kmers of size winsize over an msg with 'infinite' non repeated alphabet.
seq-filterclj
(seq-filter [id sq _ qc]
&
{:keys [qc-ctpt winsize ent-ctpt]
:or {qc-ctpt 13 winsize 10 ent-ctpt 3.12}})trim-endsclj
(trim-ends [gcnt id gsq gqc qc% :as rec] pretrim min-len sqc% marker)cljdoc is a website building & hosting documentation for Clojure/Script libraries
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