Add a function to clone bam reader.

chrovis · Apr 5, 2017 · 1949fec · 1949fec
1 parent 2b915b9
commit 1949fec
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Showing 3 changed files with 15 additions and 2 deletions.
diff --git a/src/cljam/bam.clj b/src/cljam/bam.clj
@@ -9,6 +9,11 @@
   [f & option]
   (bam-core/reader f option))
 
+(defn ^BAMReader clone-reader
+  "Clones bam reader sharing persistent objects."
+  [r]
+  (bam-core/clone-reader r))
+
 (defn ^BAMWriter writer
   "Returns BAM file writer of f."
   [f]

diff --git a/src/cljam/bam/core.clj b/src/cljam/bam/core.clj
@@ -34,7 +34,15 @@
     (let [{:keys [header refs]} (reader/load-headers data-rdr)
           index-delay (delay (bam-index f :ignore ignore-index))]
       (BAMReader. (.getAbsolutePath (file f))
-                  header refs rdr data-rdr index-delay))))
+                  header refs rdr data-rdr index-delay (.getFilePointer rdr)))))
+
+(defn ^BAMReader clone-reader
+  "Clones bam reader sharing persistent objects."
+  [^BAMReader rdr]
+  (let [bgzf-rdr (BGZFInputStream. (file (.f rdr)))
+        data-rdr (DataInputStream. bgzf-rdr)]
+    (.seek bgzf-rdr (.start-pos rdr))
+    (BAMReader. (.f rdr) (.header rdr) (.refs rdr) bgzf-rdr data-rdr (.index-delay rdr) (.start-pos rdr))))
 
 (extend-type BAMReader
   cljam.io/ISAMReader

diff --git a/src/cljam/bam/reader.clj b/src/cljam/bam/reader.clj
@@ -12,7 +12,7 @@
 ;; BAMReader
 ;; ---------
 
-(deftype BAMReader [f header refs reader data-reader index-delay]
+(deftype BAMReader [f header refs reader data-reader index-delay start-pos]
   Closeable
   (close [this]
     (.close ^Closeable (.reader this))))