Add support for random reading of bgzipped FASTA files. #174
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ghost
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@@ Coverage Diff @@
## master #174 +/- ##
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- Coverage 86.9% 86.86% -0.04%
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Files 73 74 +1
Lines 5683 5750 +67
Branches 482 492 +10
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+ Hits 4939 4995 +56
- Misses 262 263 +1
- Partials 482 492 +10
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athos
reviewed
Aug 19, 2019
src/cljam/io/util/bgzf/gzi.clj
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| (bit-and diff 0xffff)))) | ||
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| (defn comp->uncomp | ||
| "Returns a uncompressed offset for a given virtual file offset" |
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Suggested change
| "Returns a uncompressed offset for a given virtual file offset" | |
| "Returns an uncompressed offset for a given virtual file offset." |
r6eve
reviewed
Aug 19, 2019
src/cljam/io/fasta/reader.clj
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| (:import [java.io RandomAccessFile InputStream] | ||
| [cljam.io.fasta-index.core :as fasta-index] | ||
| [cljam.io.util.bgzf.gzi :as gzi] | ||
| [cljam.io.util.bgzf :as bgzf]) |
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cljam.io.util.bgzf is never used.
athos
approved these changes
Aug 20, 2019
r6eve
reviewed
Aug 20, 2019
src/cljam/io/util/bgzf/gzi.clj
Outdated
| (let [off (unsigned-bit-shift-right compressed-offset 16) | ||
| [uncompressed] (->> gzi | ||
| rseq | ||
| (filter (fn [[u c]] (= (long c) off))) |
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u is never used. https://guide.clojure.style/#underscore-for-unused-bindings
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Summary
This PR adds support for random reading of bgzip-compressed FASTA files.
cljam.io.sequence/read-sequencenow works onfa.gzfiles iffa.gz.faiandfa.gz.gziexist..gziis a file format for storing BGZF indices as a list of pairs (compressed offset, uncompressed offset).Note that this implementation does not support indexing FASTA without
.gzifile.Tests
lein check✅lein test :all✅lein cloverage✅