Merge pull request #313 from chrovis/feature/cram-writer

Add CRAM writer (alpha)

src/cljam/io/cram.clj

@@ -1,10 +1,11 @@
 (ns cljam.io.cram
-  "Alpha - subject to change. Provides functions for reading from a CRAM file."
+  "Alpha - subject to change. Provides functions for reading and writing a CRAM file."
   (:refer-clojure :exclude [indexed?])
   (:require [cljam.io.cram.core :as cram]
             [cljam.io.protocols :as protocols]
             [cljam.io.util :as io-util])
-  (:import [cljam.io.cram.reader CRAMReader]))
+  (:import [cljam.io.cram.reader CRAMReader]
+           [cljam.io.cram.writer CRAMWriter]))
 
 (defn reader
   "Creates a CRAM reader depending on the argument f: If f is a file or a string
@@ -47,3 +48,31 @@
   function immediately realizes a delayed index."
   [rdr]
   (protocols/indexed? rdr))
+
+(defn writer
+  "Creates a new CRAM writer that writes to a CRAM file f.
+
+  The function also takes an optional argument `option`, which is a map that
+  consists of:
+    - reference: A string representing the path to the reference file, or
+                 a sequence reader that reads sequences from the reference file.
+                 This may be omitted only when the CRAM file to be read does not
+                 require a reference file."
+  (^CRAMWriter [f] (writer f {}))
+  (^CRAMWriter [f option] (cram/writer f option)))
+
+(defn write-header
+  "Writes header to the CRAM file."
+  [wtr header]
+  (protocols/write-header wtr header))
+
+(defn write-refs
+  "Does nothing. This exists only for the sake of compatibility with other
+  alignment writers."
+  [wtr refs]
+  (protocols/write-refs wtr refs))
+
+(defn write-alignments
+  "Writes alignments to the CRAM file."
+  [wtr alns header]
+  (protocols/write-alignments wtr alns header))

src/cljam/io/cram/core.clj

@@ -2,12 +2,14 @@
   (:require [cljam.io.crai :as crai]
             [cljam.io.cram.reader :as reader]
             [cljam.io.cram.seq-resolver :as resolver]
+            [cljam.io.cram.writer :as writer]
             [cljam.io.sam.util.refs :as util.refs]
             [cljam.io.util.byte-buffer :as bb]
             [cljam.util :as util]
             [clojure.java.io :as cio]
             [clojure.string :as str])
   (:import [cljam.io.cram.reader CRAMReader]
+           [cljam.io.cram.writer CRAMWriter]
            [java.io FileNotFoundException]
            [java.net URL]
            [java.nio.channels FileChannel]
@@ -71,3 +73,19 @@
     (reader/read-file-definition rdr')
     (reader/skip-container rdr')
     rdr'))
+
+(defn writer
+  "Creates a new CRAM writer that writes to a CRAM file f.
+
+  Takes an option map as the second argument. An option map consists of:
+    - reference: a string representing the path to a reference file"
+  ^CRAMWriter [f {:keys [reference]}]
+  (let [file (cio/file f)
+        url (cio/as-url file)
+        url' (str url)
+        file-id (subs url' 0 (min 20 (count url')))
+        out (cio/output-stream file)
+        seq-resolver (some-> reference resolver/seq-resolver resolver/cached-resolver)
+        wtr (writer/->CRAMWriter url out seq-resolver)]
+    (writer/write-file-definition wtr file-id)
+    wtr))