(defn read-index
[f refs]
(let [refs (vec refs)]
(with-open [rdr (io/reader (util/compressor-input-stream f))]
(->> (line-seq rdr)
(map (fn [line]
(let [[^long seq-id ^long start ^long span container-offset slice-offset size]
(map #(Long/parseLong %) (str/split line #"\t"))
unmapped? (neg? seq-id)]
{:chr (if unmapped? "*" (:name (nth refs seq-id)))
:start (if unmapped? 0 start)
:end (if unmapped? 0 (+ start span))
:container-offset container-offset
:slice-offset slice-offset
:size size})))
intervals/index-intervals))))