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Issue #61 (3) Examine result file of cljam level test #70

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merged 1 commit into from
Apr 29, 2017
Merged

Issue #61 (3) Examine result file of cljam level test #70

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10 changes: 7 additions & 3 deletions test/cljam/t_cli.clj
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,9 @@
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[clojure.java.io :as io]
[cljam.cli :as cli])
[cljam.cli :as cli]
[cljam.io :as cio]
[cljam.bam :as bam])
(:import [java.io PrintStream]))

(defmacro with-out-file
Expand Down Expand Up @@ -132,8 +134,10 @@
(with-out-file temp-out (cli/level [test-bam-file temp-bam]))))
(is (not-throw? (with-out-file temp-out (cli/level [test-sorted-bam-file
temp-bam]))))
;; TODO: examine contents of temp-bam
))
(with-open [rdr (bam/reader temp-bam :ignore-index true)]
(is (= (map #(first (keep :LV (:options %)))
(cio/read-alignments rdr))
test-sorted-bam-levels)))))

(deftest about-run
(with-before-after {:before (prepare-cache!)
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14 changes: 14 additions & 0 deletions test/cljam/t_common.clj
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Original file line number Diff line number Diff line change
Expand Up @@ -307,6 +307,20 @@
{:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30], :size 75}
{:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30], :size 74}])

(def test-sorted-bam-levels
[{:type "i", :value 0}
{:type "i", :value 1}
{:type "i", :value 2}
{:type "i", :value 2}
{:type "i", :value 0}
{:type "i", :value 0}
{:type "i", :value 0}
{:type "i", :value 1}
{:type "i", :value 2}
{:type "i", :value 3}
{:type "i", :value 4}
{:type "i", :value 5}])

(def test-fa
[{:rname "ref", :offset 5, :seq "AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT", :blen 45}
{:rname "ref2", :offset 57, :seq "aggttttataaaacaattaagtctacagagcaactacgcg", :blen 40}])
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