BED reader/writer #73
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Codecov Report
@@ Coverage Diff @@
## master #73 +/- ##
==========================================
+ Coverage 82.8% 82.92% +0.12%
==========================================
Files 59 59
Lines 3774 3795 +21
Branches 410 409 -1
==========================================
+ Hits 3125 3147 +22
Misses 239 239
+ Partials 410 409 -1
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|
totakke
reviewed
May 10, 2017
src/cljam/bed.clj
Outdated
| @@ -67,6 +86,25 @@ | |||
| (defn- serialize-bed | |||
| "Serialize bed fields into string." | |||
| [m] | |||
| {:pre [(and (:chr m) (:start m) (:end m)) | |||
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and is not needed because all items in :pre vector are combined with and.
src/cljam/bed.clj
Outdated
| (if-let [xs (:block-starts m)] (= (+ (last xs) (last (:block-sizes m))) (- (:end m) (:start m))) true) | ||
| ;; The final blockStart position plus the final blockSize value must equal chromEnd. | ||
| (if-let [xs (:block-starts m)] (apply <= (mapcat (fn [a b] [a (+ a b)]) xs (:block-sizes m))) true) | ||
| ;; Blocks may not overlap. |
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I think a comment should be placed just before a related predicate.
{:pre [;; First 3 fields are required.
(:chr m) (:start m) (:end m)
;; The chromEnd base is not included in the display of the feature.
(< (:start m) (:end m))
...
]}
src/cljam/bed.clj
Outdated
| (close [this] | ||
| (.close ^Closeable (.writer this)))) | ||
|
|
||
| (defn ^BEDReader reader [f] |
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Please add docstring. Also writer.
alumi
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Thank you for the review! I've added a commit. |
totakke
approved these changes
May 10, 2017
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Added reader/writer for BED file format.
We can now read/write BED file compressed with gzip and bzip2.