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Provide a default file format version for BCF #170

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merged 4 commits into from Jul 3, 2019
Merged

Provide a default file format version for BCF #170

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a4104f4
Add a test case for the default file format version of BCF
alumi Jul 1, 2019
54b217e
Use VCFv4.3 as a default file format version of BCF
alumi Jul 1, 2019
93d87ee
Use _ for an unused local binding
alumi Jul 2, 2019
584c4bf
Use openjdk 8, 11, 12 and ea for CI
alumi Jul 3, 2019
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8 changes: 6 additions & 2 deletions src/cljam/io/bcf/writer.clj
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Expand Up @@ -22,6 +22,7 @@
(write-variants [this variants]
(write-variants this variants)))

(def ^:private ^:const default-fileformat "VCFv4.3")
(def ^:private ^:const bcf-meta-keys
[:fileformat :file-date :source :reference :contig :phasing :info :filter
:format :alt :sample :pedigree])
Expand Down Expand Up @@ -86,8 +87,11 @@
(WRITING-BCF))"
[f meta-info header]
(let [bos (bgzf/bgzf-output-stream f)
dos (DataOutputStream. bos)]
(doto (BCFWriter. (util/as-url f) (index-meta meta-info) header dos)
dos (DataOutputStream. bos)
indexed-meta (->> meta-info
(merge {:fileformat default-fileformat})
index-meta)]
(doto (BCFWriter. (util/as-url f) indexed-meta header dos)
(write-file-header))))

(defn- value-type
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13 changes: 13 additions & 0 deletions test/cljam/io/bcf/writer_test.clj
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Expand Up @@ -267,3 +267,16 @@
0x17 0x43
0x00]
[]]])))

(deftest default-meta-info
(let [tmp (File/createTempFile "default-meta-info" ".bcf")
header ["CHROM" "POS" "ID" "REF" "ALT" "QUAL" "FILTER" "INFO"]
s (->> ["##fileformat=VCFv4.3"
"##FILTER=<ID=PASS,Description=\"All filters passed\",IDX=0>"
(str "#" (cstr/join \tab header) \newline (char 0))]
(cstr/join \newline))
_ (with-open [w (bcf-writer/writer tmp {} header)])
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bytes (bb->seq (bgzf->bb tmp))]
(is (= (concat (.getBytes "BCF\2\2") [(.length s) 0 0 0] (.getBytes s))
bytes))
(.delete tmp)))