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Yf collect duplicate metrics #1424

Merged
merged 5 commits into from
Nov 19, 2019
Merged

Yf collect duplicate metrics #1424

merged 5 commits into from
Nov 19, 2019

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yfarjoun
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A CLP to collect MarkDuplicate Metrics on a file that already has had its duplicate marked. Useful when you want to have the duplicate metrics of a file but do not want to re-preprocess it. Does NOT calculate OPTICAL_DUPLICATES.

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Yossi Farjoun added 2 commits November 11, 2019 15:35
…y been duplicate-marked.

- includes some refactoring to avoid code duplication.
- added license to files that were missing it
- testing using the full MarkDuplicates testing suite.
@@ -158,13 +158,12 @@
*
* @param libraryIdGenerator
*/
protected void finalizeAndWriteMetrics(final LibraryIdGenerator libraryIdGenerator) {
static public void finalizeAndWriteMetrics(final LibraryIdGenerator libraryIdGenerator, final MetricsFile<DuplicationMetrics, Double> file, final File metricsFile) {
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Could you rename 'file' with a more informative name?

*
*/
@CommandLineProgramProperties(
summary = CollectDuplicateMetrics.USAGE_SUMMARY + CollectDuplicateMetrics.USAGE_DETAILS,
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Probably should put some whitespace between USAGE_SUMMARY and USAGE_DETAIL here.

@yfarjoun yfarjoun merged commit f6b03af into master Nov 19, 2019
@yfarjoun yfarjoun deleted the yf_collect_duplicate_metrics branch November 19, 2019 20:42
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3 participants