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Utility functions for SAM optional fields.
| (ns cljam.io.sam.util.option
(:require [clojure.string :as cstr]
[proton.core :as p]))
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parse
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|
| (defn- parse-tag-single [val-type val']
(case val-type
\Z val'
\A (first val')
\I (p/as-long val')
\i (p/as-long val')
\s (p/as-long val')
\S (p/as-long val')
\c (p/as-long val')
\C (p/as-long val')
\f (p/as-double val')
\H (p/hex->bytes val')
(-> "Unrecognized tag type: %s, for value: %s"
(format val-type val')
Exception.
throw)))
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Parses an optional field string.
| (defn parse-optional-field
[op]
(let [[tag val-type-str val'] (cstr/split op #":" 3)
val-type (first val-type-str)]
{(keyword tag) {:type val-type-str
:value (if (= val-type \B)
val'
(parse-tag-single val-type val'))}}))
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stringify
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Converts a sequence of optional fields to a string.
| (defn stringify-optional-fields
[options]
(->> options
(map
(fn [op]
(let [[tag {:keys [value] type' :type}] (first (seq op))]
(cstr/join \: [(name tag) type' value]))))
(cstr/join \tab)))
|
|
accessors
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Returns a value of an optional field named tag of an alignment.
| (defn value-for-tag
[tag aln]
(:value (some tag (:options aln))))
|
|
CIGAR string of the mate alignment.
| (def
^{:doc
:arglists '([aln])}
mate-cigar
(partial value-for-tag :MC))
|
|
Score of the alignment.
| (def
^{:doc
:arglists '([aln])}
score
(partial value-for-tag :AS))
|
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Barcode sequence.
| (def
^{:doc
:arglists '([aln])}
barcode
(partial value-for-tag :BC))
|
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Edit distance from reference of the alignment.
| (def
^{:doc
:arglists '([aln])}
edit-distance
(partial value-for-tag :NM))
|
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Parse mismatching positions in the SAM optional fields. Returns a sequence
consisting of vectors which are one of [:match matching-length],
[:mismatch a-reference-base-char] and [:deletion reference-bases-string].
| (defn parse-mismatching-positions-str
[s]
(when s
(let [[_ head tail] (re-matches #"(\d+)(.*)" s)]
(->> (re-seq #"(([A-Z])|\^([A-Z]+))(\d+)" tail)
(mapcat
(fn [[_ _ mismatch deletion match]]
[(if mismatch
[:mismatch (first mismatch)]
[:deletion deletion])
[:match (p/as-long match)]]))
(cons [:match (p/as-long head)])))))
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Mismatching positions and bases of the alignment.
| (def
^{:doc
:arglists '([aln])}
mismatching-positions
(comp parse-mismatching-positions-str (partial value-for-tag :MD)))
|
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Ratio of the primary alignment score and the alternative one.
| (def
^{:doc
:arglists '([aln])}
primary-to-alt-score
(partial value-for-tag :pa))
|
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Parse serialized supplementary alignments.
| (defn parse-supplementary-alignments-str
[s]
(when s
(->> (re-seq #"(\S+?),(\d+),([+-]),((?:\d+[MIDSH])+),(\d+),(\d+);" s)
(map (fn [[_ & rests]]
(-> [:rname :pos :strand :cigar :mapq :edit-distance]
(zipmap rests)
(update :pos p/as-long)
(update :mapq p/as-long)
(update :strand (fn [^String strand]
(case (.charAt strand 0)
\+ :forward
\- :reverse)))
(update :edit-distance p/as-long)))))))
|
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List of supplementary alignments.
| (def
^{:doc
:arglists '([aln])}
supplementary-alignments
(comp parse-supplementary-alignments-str (partial value-for-tag :SA)))
|
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Parse serialized supplementary alignments.
| (defn parse-alternative-hits-str
[s]
(when s
(->> (re-seq #"(\S+?),([+-]?\d+),((?:\d+[MIDSH])+),(\d+);" s)
(map (fn [[_ & rests]]
(-> (zipmap [:rname :pos :cigar :edit-distance] rests)
(update :pos p/as-long)
(update :edit-distance p/as-long)))))))
|
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List of alternative alignments.
| (def
^{:doc
:arglists '([aln])}
alternative-hits
(comp parse-alternative-hits-str (partial value-for-tag :XA)))
|
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Suboptimal alignment score.
| (def
^{:doc
:arglists '([aln])}
suboptimal-score
(partial value-for-tag :XS))
|
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Name of read group of the alignment.
| (def
^{:doc
:arglists '([aln])}
read-group
(partial value-for-tag :RG))
|
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Comment of reference sequence.
| (def
^{:doc
:arglists '([aln])}
ref-comment
(partial value-for-tag :XR))
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