Fix a bug in twobit reader.

chrovis · Mar 8, 2017 · e6e97fb · e6e97fb
1 parent 79e7b4c
commit e6e97fb
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/src/cljam/twobit.clj b/src/cljam/twobit.clj
@@ -108,8 +108,8 @@
       (.readFully ^RandomAccessFile (.reader rdr) ba)
       (dotimes [out-pos (inc (- end' start'))]
         (let [ref-pos (+ out-pos start')
-              ba-pos (quot (- ref-pos (max 1 start')) 4)
-              bit-pos (mod (- ref-pos (max 1 start')) 4)]
+              ba-pos (- (quot (dec ref-pos) 4) start-offset)
+              bit-pos (mod (dec ref-pos) 4)]
           (if (<= 1 ref-pos len)
             (.put cb (.charAt ^String (twobit-to-str (+ (aget ba ba-pos) 128)) bit-pos))
             (.put cb \N))))

diff --git a/test/cljam/t_twobit.clj b/test/cljam/t_twobit.clj
@@ -8,6 +8,10 @@
    (tb/read-sequence r {:chr "ref"}) => "AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT"
    (tb/read-sequence r {:chr "ref2"}) => "AGGTTTTATAAAACAATTAAGTCTACAGAGCAACTACGCG"
    (tb/read-sequence r {:chr "ref2" :mask? true}) => "aggttttataaaacaattaagtctacagagcaactacgcg"
+   (for [i (range 1 45) j (range i 46)]
+     (tb/read-sequence r {:chr "ref" :start i :end j}))
+   => (for [i (range 1 45) j (range i 46)]
+        (subs "AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT" (dec i) j))
    (tb/read-sequence r {:chr "ref" :start 1 :end 4}) => "AGCA"
    (tb/read-sequence r {:chr "ref" :start 0 :end 4}) => "NAGCA"
    (tb/read-sequence r {:chr "ref" :start 41 :end 50}) => "GCCATNNNNN"
@@ -22,6 +26,10 @@
    (tb/read-sequence r {:chr "ref"}) => "NNNNNGTTAGATAAGATAGCNNTGCTAGTAGGCAGTCNNNNCCAT"
    (tb/read-sequence r {:chr "ref2"}) => "AGNNNTTATAAAACAATTANNNCTACAGAGCAACTANNNN"
    (tb/read-sequence r {:chr "ref2" :mask? true}) => "agNNNttataaaacaattaNNNctacagagcaactaNNNN"
+   (for [i (range 1 45) j (range i 46)]
+     (tb/read-sequence r {:chr "ref" :start i :end j}))
+   => (for [i (range 1 45) j (range i 46)]
+        (subs "NNNNNGTTAGATAAGATAGCNNTGCTAGTAGGCAGTCNNNNCCAT" (dec i) j))
    (tb/read-sequence r {:chr "ref" :start 1 :end 4}) => "NNNN"
    (tb/read-sequence r {:chr "ref" :start 0 :end 4}) => "NNNNN"
    (tb/read-sequence r {:chr "ref" :start 41 :end 50}) => "NCCATNNNNN"