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tabix.clj
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tabix.clj
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(ns cljam.io.tabix
"Alpha - subject to change.
Reader of a TABIX format file."
(:require [cljam.io.util.bgzf :as bgzf]
[cljam.io.util.lsb :as lsb])
(:import java.util.Arrays
[java.io DataInputStream IOException]))
(def tabix-magic "TBI\1")
(defn- read-seq
[buf len]
(loop [i 0, j 0, seq* []]
(if (< i len)
(if (zero? (nth buf i))
(let [ba-len (- i j)
ba (byte-array ba-len)]
(System/arraycopy buf j ba 0 ba-len)
(recur (inc i) (inc i) (conj seq* (String. ba))))
(recur (inc i) j seq*))
seq*)))
(defn- read-chunk
[^DataInputStream rdr]
{:beg (lsb/read-long rdr)
:end (lsb/read-long rdr)})
(defn- read-bin
[^DataInputStream rdr]
(let [bin (lsb/read-int rdr)
n-chunk (lsb/read-int rdr)]
{:bin bin
:chunks (doall (map (fn [_] (read-chunk rdr)) (range n-chunk)))}))
(defn- read-index*
[^DataInputStream rdr]
(when-not (Arrays/equals ^bytes (lsb/read-bytes rdr 4) (.getBytes ^String tabix-magic))
(throw (IOException. "Invalid TABIX file")))
(let [n-seq (lsb/read-int rdr)
preset (lsb/read-int rdr)
sc (lsb/read-int rdr)
bc (lsb/read-int rdr)
ec (lsb/read-int rdr)
meta (lsb/read-int rdr)
skip (lsb/read-int rdr)
len (lsb/read-int rdr)
buf (lsb/read-bytes rdr len)
seq (read-seq buf len)
index (loop [i 0
bin-index []
linear-index []]
(if (< i n-seq)
(let [n-bin (lsb/read-int rdr)
new-bin-index (doall (map (fn [_] (read-bin rdr)) (range n-bin)))
n-linear-index (lsb/read-int rdr)
new-linear-index (doall (map (fn [_] (lsb/read-long rdr)) (range n-linear-index)))]
(recur (inc i)
(conj bin-index new-bin-index)
(conj linear-index new-linear-index)))
[bin-index linear-index]))]
{:n-seq n-seq, :preset preset, :sc sc, :bc bc, :ec ec, :meta meta,
:skip skip, :seq seq ,:bin-index (first index), :linear-index (last index)}))
(defn read-index
[f]
(with-open [r (DataInputStream. (bgzf/bgzf-input-stream f))]
(read-index* r)))