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Utility functions for SAM references.
| (ns cljam.io.sam.util.refs
(:require [clojure.set :as cset]))
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Returns a reference sequence from the sam header.
| (defn make-refs
[hdr]
(map
#(cset/rename-keys
%
{:SN :name, :LN :len, :AH :alt, :AS :assembly,
:M5 :md5, :SP :species, :UR :uri})
(:SQ hdr)))
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|
| (defn- ref-id*
[refs name']
(some #(when (= name' (:name (second %))) (first %))
(map-indexed vector refs)))
|
|
Returns reference ID from the reference sequence and the specified reference
name. If not found, returns nil.
| (def ref-id
(memoize ref-id*))
|
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Returns a reference name from the reference ID. Returns nil if id is not
mapped.
| (defn ref-name
[refs ^long id]
(when (<= 0 id (dec (count refs)))
(:name (nth refs id))))
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Returns the first reference which has the specified name.
| (defn ref-by-name
[refs name']
(some #(when (= (:name %) name') %) refs))
|
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