The core of BAM features. | (ns cljam.io.bam.core
(:require [clojure.string :as cstr]
[cljam.io.bam [common :as common]
[reader :as reader]
[writer :as writer]]
[cljam.io.bam-index :as bai]
[cljam.io.util.bgzf :as bgzf]
[cljam.io.util.lsb :as lsb]
[cljam.util :as util])
(:import java.util.Arrays
[java.io DataInputStream DataOutputStream IOException FileNotFoundException]
cljam.io.bam.reader.BAMReader
cljam.io.bam.writer.BAMWriter)) |
Reading | |
Loads an index file (BAI) for the given BAM URL. | (defn- bam-index
[bam-url]
(or (->> ["$1.bai" ".bai" "$1.BAI" ".BAI"]
(eduction
(comp
(map #(cstr/replace (str bam-url) #"(?i)(\.bam)$" %))
(map util/as-url)
(keep #(try (bai/bam-index %) (catch FileNotFoundException _)))))
first)
(throw (FileNotFoundException.
(str "Could not find BAM Index file for " bam-url))))) |
Creates a | (defn ^BAMReader reader
[f]
(let [rdr (bgzf/bgzf-input-stream f)
data-rdr (DataInputStream. rdr)]
(when-not (Arrays/equals ^bytes (lsb/read-bytes data-rdr 4) (.getBytes ^String common/bam-magic))
(throw (IOException. "Invalid BAM file")))
(let [{:keys [header refs]} (reader/load-headers data-rdr)
index-delay (delay (bam-index (util/as-url f)))]
(BAMReader. (util/as-url f)
header refs rdr data-rdr index-delay (.getFilePointer rdr))))) |
Clones bam reader sharing persistent objects. | (defn ^BAMReader clone-reader
[^BAMReader rdr]
(let [bgzf-rdr (bgzf/bgzf-input-stream (.url rdr))
data-rdr (DataInputStream. bgzf-rdr)]
(.seek bgzf-rdr (.start-pos rdr))
(BAMReader. (.url rdr) (.header rdr) (.refs rdr) bgzf-rdr data-rdr (.index-delay rdr) (.start-pos rdr)))) |
Writing | |
(defn ^BAMWriter writer
([f] (writer f false))
([f create-index?]
(let [index (if create-index? {:no-coordinate-alns 0} false)
w (bgzf/bgzf-output-stream f)]
(BAMWriter. (util/as-url f)
w
(DataOutputStream. w)
(atom nil)
(atom index))))) | |