Add FASTAWriter and TwoBitWriter. #79
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Codecov Report
@@ Coverage Diff @@
## master #79 +/- ##
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+ Coverage 82.07% 82.42% +0.34%
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Files 59 62 +3
Lines 3922 4113 +191
Branches 423 439 +16
==========================================
+ Hits 3219 3390 +171
- Misses 280 284 +4
- Partials 423 439 +16
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totakke
reviewed
May 30, 2017
src/cljam/twobit/writer.clj
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| @@ -0,0 +1,162 @@ | |||
| (ns cljam.twobit.writer | |||
| (:require [clojure.java.io :as cio] | |||
| [clojure.string :as cstr] | |||
src/cljam/twobit/reader.clj
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| ([rdr] | ||
| (read-all-sequences rdr {})) | ||
| ([rdr option] | ||
| (for [{:keys [name offset]} (.file-index rdr)] |
src/cljam/twobit/reader.clj
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| [clojure.java.io :as cio] | ||
| [cljam.io :as io] | ||
| [cljam.lsb :as lsb] | ||
| [cljam.util :as util]) |
There was a problem hiding this comment.
cstr and util are not used in this ns.
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Thank you for your review! |
totakke
approved these changes
May 30, 2017
|
Good, thanks. |
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Summary
This PR adds (naive implementation of) writers for FASTA and 2bit format.
Changes
ISequenceWritertocljam.io.cljam.fasta.writer.FASTAWriterandcljam.twobit.writer.TwoBitWriter.cljam.twobittocljam.twobit.reader.read-all-sequencestoISequenceReader.ISequenceReader.Affected components
cljam.fastacljam.twobitNotes
Performance is not yet optimized.