Merge pull request #60 from ayamada/feature/add-tests-for-coverage-on…

…ly-fixes-s

Add many tests / Remove unused codes about `slurp` fasta

src/cljam/fasta/core.clj

@@ -1,5 +1,5 @@
 (ns cljam.fasta.core
-  (:refer-clojure :exclude [read slurp])
+  (:refer-clojure :exclude [read])
   (:require [clojure.java.io :as io]
             [cljam.util :as util]
             [cljam.fasta-index.core :as fasta-index]
@@ -55,13 +55,6 @@
   [rdr]
   (reader/reset rdr))
 
-(defn slurp
-  "Opens a reader on a FASTA file and reads all its contents, returning
-  a sequence about the data."
-  [f]
-  (with-open [r (reader f)]
-    (doall (reader/read r))))
-
 (defn sequential-read
   [f]
   (with-open [stream (util/compressor-input-stream f)]

src/cljam/fasta/reader.clj

@@ -1,5 +1,5 @@
 (ns cljam.fasta.reader
-  (:refer-clojure :exclude [read slurp])
+  (:refer-clojure :exclude [read])
   (:require [clojure.string :as cstr]
             [cljam.util :refer [graph?]]
             [cljam.util.fasta :refer [header-line? parse-header-line]]

test/cljam/t_bam.clj

@@ -1,13 +1,18 @@
 (ns cljam.t-bam
   (:require [clojure.test :refer :all]
             [cljam.t-common :refer :all]
-            [clojure.java.io :refer [copy file]]
+            [clojure.java.io :refer [copy file delete-file]]
             [cljam.bam :as bam]
             [cljam.io :as io]
-            [cljam.sorter :as sorter]))
+            [cljam.bam-index.core :as bai-core]
+            [cljam.sorter :as sorter])
+  (:import [java.io IOException]))
 
 (def temp-file (str temp-dir "/test.bam"))
 (def temp-file-sorted (str temp-dir "/test.sorted.bam"))
+(def not-found-file (str temp-dir "/not-found.bam"))
+(def invalid-file-1 test-fa-file)
+(def invalid-file-2 test-tabix-file)
 
 (deftest slurp-bam
   (is (= (slurp-bam-for-test test-bam-file) test-sam)))
@@ -40,23 +45,79 @@
 ;;     (is (not-throw? (spit-bam-for-test temp-file
 ;;                                        (slurp-bam-for-test large-bam-file))))))
 
+(defn- shallow= [alns1 alns2]
+  (= (map #(select-keys % [:rname :pos]) alns1)
+     (map #(select-keys % [:rname :pos]) alns2)))
+
+(defn- pointer= [alns1 alns2]
+  (= (map #(select-keys % [:rname :pos :flag]) alns1)
+     (map #(select-keys % [:rname :pos :flag]) alns2)))
+
 (deftest bamreader
   (with-before-after {:before (do (prepare-cache!)
                                   (spit-bam-for-test temp-file test-sam))
                       :after (clean-cache!)}
-    (let [rdr (bam/reader temp-file :ignore-index true)]
-      (is (= (io/read-refs rdr) test-sam-refs)))))
+    (with-open [rdr (bam/reader temp-file :ignore-index false)]
+      (is (= (io/read-refs rdr) test-sam-refs))
+      (is (= (io/read-alignments rdr) (:alignments test-sam))))
+    (with-open [rdr (bam/reader temp-file :ignore-index false)]
+      (is (= (io/read-refs rdr) test-sam-refs))
+      (is (thrown? Exception (io/read-alignments rdr {:chr "ref2"}))))
+    (with-open [rdr (bam/reader temp-file :ignore-index false)]
+      (is (= (io/read-refs rdr) test-sam-refs))
+      (is (= (io/read-alignments rdr {:depth :deep}) (:alignments test-sam))))
+    (with-open [rdr (bam/reader temp-file :ignore-index false)]
+      (is (= (io/read-refs rdr) test-sam-refs))
+      (is (shallow= (io/read-alignments rdr {:depth :shallow})
+                    (:alignments test-sam))))
+    (with-open [rdr (bam/reader temp-file :ignore-index false)]
+      (is (= (io/read-refs rdr) test-sam-refs))
+      (is (pointer= (io/read-alignments rdr {:depth :pointer})
+                    (:alignments test-sam))))
+    (with-open [rdr (bam/reader temp-file :ignore-index false)]
+      (is (= (io/read-refs rdr) test-sam-refs))
+      (is (= (data->clj (io/read-blocks rdr)) test-sam-data)))
+    (with-open [rdr (bam/reader temp-file :ignore-index false)]
+      (is (= (io/read-refs rdr) test-sam-refs))
+      (is (thrown? Exception (data->clj (io/read-blocks rdr {:chr "ref2"})))))))
 
-(deftest-slow bamreader-medium-file
-  (with-before-after {:before (do (prepare-cache!)
-                                  (spit-bam-for-test temp-file test-sam))
-                      :after (clean-cache!)})
-    (let [rdr (bam/reader medium-bam-file :ignore-index true)]
-      (is (= (io/read-refs rdr) medium-sam-refs))))
+(deftest bamreader-with-index
+  (with-before-after {:before (prepare-cache!)
+                      :after (clean-cache!)}
+    (with-open [rdr (bam/reader test-sorted-bam-file :ignore-index false)]
+      ;; TODO: Does not works?
+      (is (= (io/read-alignments rdr {:chr "ref2"}) [])))
+    (with-open [rdr (bam/reader test-sorted-bam-file :ignore-index false)]
+      (is (= (data->clj (io/read-blocks rdr)) test-sorted-bam-data)))
+    (with-open [rdr (bam/reader test-sorted-bam-file :ignore-index false)]
+      ;; TODO: Does not works?
+      (is (= (data->clj (io/read-blocks rdr {:chr "ref2"})) [])))))
+
+(deftest bamreader-invalid-files
+  (with-before-after {:before (prepare-cache!)
+                      :after (clean-cache!)}
+    (is (thrown? Exception (bam/reader invalid-file-1 :ignore-index true)))
+    (is (thrown? IOException (bam/reader invalid-file-2 :ignore-index true)))
+    (is (thrown? IOException (bam/reader not-found-file :ignore-index true)))))
+
+(deftest bamreader-medium-file
+  (with-before-after {:before (prepare-cache!)
+                      :after (clean-cache!)}
+    (with-open [rdr (bam/reader medium-bam-file :ignore-index true)]
+      (let [header (io/read-header rdr)
+            refs (io/read-refs rdr)
+            alns (io/read-alignments rdr)]
+        (is (= refs medium-sam-refs))
+        (with-open [w (bam/writer temp-file)]
+          (is (not-throw? (io/write-header w header)))
+          (is (not-throw? (io/write-refs w refs)))
+          (is (not-throw? (io/write-alignments w alns header)))
+          (same-file? medium-bam-file temp-file))))))
 
 (deftest-slow-heavy bamreader-large-file
   (with-before-after {:before (do (prepare-cache!)
                                   (prepare-cavia!))
                       :after (clean-cache!)}
-    (let [rdr (bam/reader large-bam-file :ignore-index true)]
-      (is (= (io/read-refs rdr) large-sam-refs)))))
+    (with-open [rdr (bam/reader large-bam-file :ignore-index true)]
+      (is (= (io/read-refs rdr) large-sam-refs))
+      (is (not-throw? (io/read-alignments rdr))))))

test/cljam/t_bam_index.clj

@@ -7,7 +7,8 @@
 ;;; bin-index
 
 (deftest bin-index-is-done-without-errors
-  (is (not-throw? (bai/bin-index test-bai-file 0))))
+  (is (not-throw? (bai/bin-index test-bai-file 0)))
+  (is (not-throw? (bai/bin-index test-bai-file 1))))
 (deftest bin-index-throws-BoundsException-for-the-invalid-given-index
   (is (thrown? Exception (bai/bin-index test-bai-file 2))))
 (deftest bin-index-returns-vector
@@ -36,10 +37,9 @@
 (deftest get-spans-returns-a-sequence-including-regions
   (let [bai* (bai/bam-index test-bai-file)]
     (is (seq? (bai/get-spans bai* 0 0 100)))
-    (is (every? #(and
-                   (= 2 (count %))
-                   (number? (first %))
-                   (number? (second %)))
+    (is (every? #(and (= 2 (count %))
+                      (number? (first %))
+                      (number? (second %)))
                 (bai/get-spans bai* 0 0 100)))))
 (deftest get-spans-returns-correct-regions
   (let [bai* (bai/bam-index test-bai-file)]

test/cljam/t_bam_indexer.clj

@@ -24,6 +24,12 @@
            (filter #(= "ref" (:rname %))
                    (:alignments test-sam-sorted-by-pos))))))
 
+(deftest about-bam-indexer-invalid-files
+  (with-before-after {:before (prepare-cache!)
+                      :after (clean-cache!)}
+    (is (thrown? Exception (bai/create-index "not-exists-file"
+                                             "not-exists-file.bai")))))
+
 (deftest about-bam-indexer-for-incomplete-alignments
   (let [f (str temp-dir "/test.incomplete.bam")
         sorted-f (str temp-dir "/test.incomplete.sorted.bam")]
@@ -46,23 +52,24 @@
       )))
 
 (deftest about-bam-indexer-small-file
-  (with-before-after {:before (do (prepare-cache!)
-                                  (fs/copy small-bam-file temp-file-sorted))
-                      :after (clean-cache!)}
-    (is (not-throw? (bai/create-index temp-file-sorted
-                                      (str temp-file-sorted ".bai"))))
-    (is (fs/exists? (str temp-file-sorted ".bai")))
-    (with-open [r (bam/reader temp-file-sorted)]
-      ;; Random read with different number of spans.
-      (is (= (count (io/read-alignments r {:chr "chr1" :start 23000000 :end 25000000 :depth :deep}))
-             14858))
-      (is (= (count (io/read-alignments r {:chr "chr1" :start 23000000 :end 24500000 :depth :deep}))
-             11424))
-      (is (= (count (io/read-alignments r {:chr "chr1" :start 23000000 :end 24000000 :depth :deep}))
-             10010))
-      (is (= (count (io/read-alignments r {:chr "chr1" :start 23000000 :end 23500000 :depth :deep}))
-             3806))
-      (is (= (count (io/read-alignments r {:chr "*"})) 0)))))
+  (doseq [n-threads [1 4]]
+    (with-before-after {:before (do (prepare-cache!)
+                                    (fs/copy small-bam-file temp-file-sorted))
+                        :after (clean-cache!)}
+      (is (not-throw? (bai/create-index temp-file-sorted
+                                        (str temp-file-sorted ".bai")
+                                        :n-threads n-threads)))
+      (is (fs/exists? (str temp-file-sorted ".bai")))
+      (with-open [r (bam/reader temp-file-sorted)]
+        ;; Random read with different number of spans.
+        (are [?param ?counts] (= (count (io/read-alignments r ?param)) ?counts)
+          {:chr "chr1" :start 23000000 :end 25000000 :depth :shallow} 14858
+          {:chr "chr1" :start 23000000 :end 25000000 :depth :pointer} 14858
+          {:chr "chr1" :start 23000000 :end 25000000 :depth :deep} 14858
+          {:chr "chr1" :start 23000000 :end 24500000 :depth :deep} 11424
+          {:chr "chr1" :start 23000000 :end 24000000 :depth :deep} 10010
+          {:chr "chr1" :start 23000000 :end 23500000 :depth :deep} 3806
+          {:chr "*"} 0)))))
 
 (deftest-slow about-bam-indexer-medium-file
   (with-before-after {:before (do (prepare-cache!)

test/cljam/t_bed.clj

@@ -23,7 +23,25 @@
     (.flush bw)
     (.toString bao)))
 
+(defn- raw-str->bed [^String s]
+  (with-open [bais (ByteArrayInputStream. (.getBytes s))
+              isr (InputStreamReader. bais)
+              br (BufferedReader. isr)]
+    (doall (bed/read-raw-fields br))))
+
+(defn- bed->raw-str [xs]
+  (with-open [bao (ByteArrayOutputStream.)
+              osw (OutputStreamWriter. bao)
+              bw (BufferedWriter. osw)]
+    (bed/write-raw-fields bw xs)
+    (.flush bw)
+    (.toString bao)))
+
 (deftest bed-file-reader-1
+  (is (= (raw-str->bed "1 0 100 N 0 + 0 0 255,0,0 2 10,90 0,10")
+         [{:chr "1" :start 0 :end 100 :name "N" :score 0 :strand :plus :thick-start 0 :thick-end 0
+           :item-rgb "255,0,0" :block-count 2 :block-sizes [10 90] :block-starts [0 10]}]))
+
   (is (= (str->bed "1 0 100 N 0 + 0 0 255,0,0 2 10,90 0,10")
          [{:chr "chr1" :start 1 :end 100 :name "N" :score 0 :strand :plus :thick-start 1 :thick-end 0
            :item-rgb "255,0,0" :block-count 2 :block-sizes [10 90] :block-starts [0 10]}]))
@@ -124,27 +142,34 @@
   (with-open [bam (bam/reader "test-resources/test.sorted.bam")]
     (letfn [(ref-pos-end [m] {:rname (:rname m) :pos (:pos m) :end (sam-util/get-end m)})
             (read-region [s] (->> (str->bed s) (mapcat #(cio/read-alignments bam %)) (map ref-pos-end)))]
-      (is (= (read-region "ref 0 6") []))
-      (is (= (read-region "ref 6 7") [{:rname "ref" :pos 7 :end 22}]))
-      (is (= (read-region "ref 7 8") [{:rname "ref" :pos 7 :end 22}]))
-      (is (= (read-region "ref 8 9")
-             [{:rname "ref" :pos 7 :end 22} {:rname "ref" :pos 9 :end 18} {:rname "ref" :pos 9 :end 14}]))
-      (is (= (read-region "ref 21 22")
-             [{:rname "ref" :pos 7 :end 22} {:rname "ref" :pos 16 :end 40}]))
-      (is (= (read-region "ref 22 23") [{:rname "ref" :pos 16 :end 40}]))
-      (is (= (read-region "ref 0 45")
-             [{:rname "ref" :pos 7  :end 22} {:rname "ref" :pos 9  :end 18} {:rname "ref" :pos 9  :end 14}
-              {:rname "ref" :pos 16 :end 40} {:rname "ref" :pos 29 :end 33} {:rname "ref" :pos 37 :end 45}])))))
+      (are [?region-str ?result] (= (read-region ?region-str) ?result)
+        "ref 0 6" []
+        "ref 6 7" [{:rname "ref" :pos 7 :end 22}]
+        "ref 7 8" [{:rname "ref" :pos 7 :end 22}]
+        "ref 8 9" [{:rname "ref" :pos 7 :end 22}
+                   {:rname "ref" :pos 9 :end 18}
+                   {:rname "ref" :pos 9 :end 14}]
+        "ref 21 22" [{:rname "ref" :pos 7 :end 22}
+                     {:rname "ref" :pos 16 :end 40}]
+        "ref 22 23" [{:rname "ref" :pos 16 :end 40}]
+        "ref 0 45" [{:rname "ref" :pos 7  :end 22}
+                    {:rname "ref" :pos 9  :end 18}
+                    {:rname "ref" :pos 9  :end 14}
+                    {:rname "ref" :pos 16 :end 40}
+                    {:rname "ref" :pos 29 :end 33}
+                    {:rname "ref" :pos 37 :end 45}]))))
 
 (deftest bed-reader-and-fasta-reader
   (with-open [fa (fa/reader "test-resources/medium.fa")]
     (comment "chr1" "TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC...")
     (letfn [(read-region [s] (->> (str->bed s) (map #(fa/read-sequence fa %))))]
-      (is (= (read-region "1 0 1") ["T"]))
-      (is (= (read-region "1 0 10") ["TAACCCTAAC"]))
-      (is (= (read-region "1 0 10\n1 10 20") ["TAACCCTAAC" "CCTAACCCTA"])))))
+      (are [?region-str ?result] (= (read-region ?region-str) ?result)
+        "1 0 1" ["T"]
+        "1 0 10" ["TAACCCTAAC"]
+        "1 0 10\n1 10 20" ["TAACCCTAAC" "CCTAACCCTA"]))))
 
 (deftest bed-writer
+  (is (= (bed->raw-str (raw-str->bed "1 0 10")) "1 0 10"))
   (is (= (bed->str (str->bed "1 0 1")) "chr1 0 1"))
   (is (= (bed->str (str->bed "1 0 10")) "chr1 0 10"))
   (is (= (bed->str (str->bed "1 0 1\n1 1 2")) "chr1 0 1\nchr1 1 2"))