Add metric builder and sorter #826

nh13 · 2022-04-20T07:54:42Z

Added a new class MetricSorter that's useful when we want to sort metrics but cannot hold them all in memory. Leverages Sorter.

src/main/scala/com/fulcrumgenomics/util/Metric.scala

codecov-commenter · 2022-04-20T23:54:01Z

Codecov Report

Merging #826 (b0b942e) into main (57a72b4) will decrease coverage by 0.14%.
The diff coverage is 72.50%.

❗ Current head b0b942e differs from pull request most recent head 45b68d6. Consider uploading reports for the commit 45b68d6 to get more accurate results

@@            Coverage Diff             @@
##             main     #826      +/-   ##
==========================================
- Coverage   95.67%   95.53%   -0.15%     
==========================================
  Files         125      127       +2     
  Lines        7234     7251      +17     
  Branches      489      501      +12     
==========================================
+ Hits         6921     6927       +6     
- Misses        313      324      +11

Flag	Coverage Δ
unittests	`95.53% <72.50%> (-0.15%)`	⬇️

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Impacted Files	Coverage Δ
.../scala/com/fulcrumgenomics/util/MetricSorter.scala	`0.00% <0.00%> (ø)`
...scala/com/fulcrumgenomics/util/MetricBuilder.scala	`79.31% <79.31%> (ø)`
...c/main/scala/com/fulcrumgenomics/util/Metric.scala	`95.08% <100.00%> (-1.08%)`	⬇️

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nh13 · 2022-04-21T15:54:43Z

src/main/scala/com/fulcrumgenomics/util/MetricBuilder.scala

+    * @param lineNumber optionally, the line number when building a metric from a line in a file
+    * @return
+    */
+  def fromLine(line: String, delim: String = Metric.DelimiterAsString, lineNumber: Option[Int] = None): T = {


Note: need to have different names for each of the from* methods because I want lineNumber to default to None, and I can't have multiple functions with the same name AND each with default values.

nh13 · 2022-04-21T23:16:35Z

Relies on fulcrumgenomics/commons#82

nh13 · 2022-04-21T23:16:56Z

src/main/scala/com/fulcrumgenomics/util/MetricBuilder.scala

+    * @return a new instance of type [[T]]
+    */
+  def fromArgMap(argMap: Map[String, String], lineNumber: Option[Int] = None): T = {
+    reflectiveBuilder.reset() // reset the arguments to their initial values


Relies on fulcrumgenomics/commons#82

Add metrics sorter

b7c9a89

nh13 commented Apr 20, 2022

View reviewed changes