(ns cljam.io.vcf.util.check (:require [cljam.io.sequence :as io-seq])) | |
Checks if a REF allele matches the reference sequence. | (defn same-ref?
[seq-reader {:keys [chr ^long pos ^String ref]}]
(let [ref-len (.length ref)
ref-region {:chr chr :start pos :end (dec (+ pos ref-len))}
ref-seq (io-seq/read-sequence seq-reader ref-region {:mask? false})]
(and ref-seq (.equalsIgnoreCase ^String ref-seq ref)))) |