Extract depth algorithm and improve performance. #91
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Codecov Report
@@ Coverage Diff @@
## master #91 +/- ##
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+ Coverage 82.71% 82.93% +0.22%
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Files 60 60
Lines 4107 4161 +54
Branches 437 452 +15
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+ Hits 3397 3451 +54
+ Misses 273 258 -15
- Partials 437 452 +15
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totakke
reviewed
Jul 28, 2017
src/cljam/algo/depth.clj
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| [bam-reader {:keys [chr start end] :or {start 1 end Long/MAX_VALUE}} | ||
| & [{:keys [step unchecked? n-threads] :or {step default-step unchecked? false n-threads 1}}]] | ||
| {:pre [chr start end (pos? start) (pos? end) (<= start end)]} | ||
| (when-let [{:keys [len] :as r} (sam-util/ref-by-name (sam/read-refs bam-reader) chr)] |
src/cljam/algo/pileup.clj
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| "Returns a position of first alignment in left-right, or nil." | ||
| [bam-reader region] | ||
| (plp/first-pos bam-reader region)) | ||
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| (def ^:private default-pileup-option |
There was a problem hiding this comment.
default-pileup-option is no longer needed.
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Thank you for reviewing! I've just removed the unused vars. |
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Thanks |
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Changes
cljam.algo.pileup.pileup/pileupfunction tocljam.algo.depth/lazy-depth.cljam.algo.depth/depthoptimized for performance.Benchmark
Computing depth for
chr1:1-248956422BAM file containing about 3500000 alignments in the region.Environment
Results
The eager version is >10x faster.