Rename protocol IRandomReader to IRegionReader.

src/cljam/bam/reader.clj

@@ -62,7 +62,7 @@
     (if (nil? chr)
       (read-blocks-sequentially* this mode)
       (read-blocks* this chr start end)))
-  io/IRandomReader
+  io/IRegionReader
   (read-in-region [this region]
     (io/read-in-region this region {}))
   (read-in-region [this region option]

src/cljam/bcf/reader.clj

@@ -21,7 +21,7 @@
   (reader-path [this] (.f this))
   (read [this] (io/read this {}))
   (read [this option] (read-variants this option))
-  io/IRandomReader
+  io/IRegionReader
   (read-in-region [this region]
     (io/read-in-region this region {}))
   (read-in-region [this {:keys [chr start end]} option]

src/cljam/bed.clj

@@ -17,7 +17,7 @@
   (reader-path [this] (.f this))
   (read [this] (io/read this {}))
   (read [this option] (read-fields this))
-  io/IRandomReader
+  io/IRegionReader
   (read-in-region [this region]
     (io/read-in-region this region {}))
   (read-in-region [this {:keys [chr start end]} option]

src/cljam/fasta/core.clj

@@ -67,7 +67,7 @@
   (read
     ([this] (sequential-read (.f this)))
     ([this option] (sequential-read (.f this))))
-  io/IRandomReader
+  io/IRegionReader
   (read-in-region
     ([this region]
      (io/read-in-region this region {}))

src/cljam/io.clj

@@ -15,7 +15,7 @@
   (writer-path [this]
     "Returns the file's absolute path."))
 
-(defprotocol IRandomReader
+(defprotocol IRegionReader
   (read-in-region [this region] [this region option]
     "Reads contents of the file in given region."))
 

src/cljam/sam/reader.clj

@@ -20,7 +20,7 @@
     (io/read this {}))
   (read [this option]
     (read-alignments* this))
-  io/IRandomReader
+  io/IRegionReader
   (read-in-region [this region]
     (io/read-in-region this region {}))
   (read-in-region [this region option]

src/cljam/twobit.clj

@@ -135,7 +135,7 @@
      (io/read-sequence this region {}))
     (^String [this region option]
      (read-sequence this region option)))
-  io/IRandomReader
+  io/IRegionReader
   (read-in-region
     (^String [this region]
      (io/read-in-region this region {}))

src/cljam/vcf/reader.clj

@@ -23,7 +23,7 @@
   (reader-path [this] (.f this))
   (read [this] (read-variants this))
   (read [this option] (read-variants this option))
-  io/IRandomReader
+  io/IRegionReader
   (read-in-region [this region]
     (io/read-in-region this region {}))
   (read-in-region [this {:keys [chr start end]} {:keys [depth] :as option}]