Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Added a slightly more helpful error message to the reads filter #7947

Merged
merged 2 commits into from
Dec 23, 2022
Merged

Added a slightly more helpful error message to the reads filter #7947

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
413983a
added a slightly better read filtering message
jamesemery Jul 15, 2022
7791882
updating the tests to reflect the new behavior around tracking total …
jamesemery Jul 19, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
4 changes: 3 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/engine/filters/CountingReadFilter.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -201,6 +201,7 @@ public void resetFilteredCount() {
protected static final class CountingAndReadFilter extends CountingBinopReadFilter {

private static final long serialVersionUID = 1L;
protected long totalCount = 0;

private CountingAndReadFilter(final CountingReadFilter lhs, final CountingReadFilter rhs) {
super(lhs, rhs);
Expand All @@ -212,6 +213,7 @@ public boolean test(final GATKRead read) {
if (!accept) {
filteredCount++;
}
totalCount++;
return accept;
}

Expand Down Expand Up @@ -249,7 +251,7 @@ private String getSummaryLineForLevelAllAndsSimplified() {
}
}

summaryLine.append(this.getFilteredCount() + " total reads filtered");
summaryLine.append(this.getFilteredCount() + " total reads filtered out of "+ this.totalCount+ " reads processed");

return summaryLine.toString();
}
Expand Down
19 changes: 11 additions & 8 deletions src/test/java/org/broadinstitute/hellbender/engine/filters/CountingReadFilterUnitTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -329,34 +329,37 @@ public Object[][] testAndFilterSummaryLineDataProvider() {
final CountingReadFilter secondOfPair2 = new CountingReadFilter(ReadFilterLibrary.SECOND_OF_PAIR);
secondOfPair2.filteredCount = 2;

final CountingReadFilter firstOfPair1AndSecondOfPair2 = firstOfPair1.and(secondOfPair2);
final CountingReadFilter.CountingAndReadFilter firstOfPair1AndSecondOfPair2 = (CountingReadFilter.CountingAndReadFilter)firstOfPair1.and(secondOfPair2);
firstOfPair1AndSecondOfPair2.filteredCount = 3;
firstOfPair1AndSecondOfPair2.totalCount = 3;
final String andWithCountsAbove0 = "1 read(s) filtered by: FirstOfPairReadFilter \n"
+ "2 read(s) filtered by: SecondOfPairReadFilter \n"
+ "3 total reads filtered";
+ "3 total reads filtered out of 3 reads processed";

final CountingReadFilter firstOfPair1AndMappingQuality0 = firstOfPair1.and(mappingQuality0);
final CountingReadFilter.CountingAndReadFilter firstOfPair1AndMappingQuality0 = (CountingReadFilter.CountingAndReadFilter)firstOfPair1.and(mappingQuality0);
firstOfPair1AndMappingQuality0.filteredCount = 1;
firstOfPair1AndMappingQuality0.totalCount = 3;
final String andWith1CountAbove0 = "1 read(s) filtered by: FirstOfPairReadFilter \n"
+ "0 read(s) filtered by: MappingQualityAvailableReadFilter \n"
+ "1 total reads filtered";
+ "1 total reads filtered out of 3 reads processed";

final CountingReadFilter mappingQuality0AndGoodCigar0 = mappingQuality0.and(goodCigar0);
final CountingReadFilter.CountingAndReadFilter mappingQuality0AndGoodCigar0 = (CountingReadFilter.CountingAndReadFilter)mappingQuality0.and(goodCigar0);
mappingQuality0AndGoodCigar0.filteredCount = 0;
final String andWithBoth0Counts = "0 read(s) filtered by: MappingQualityAvailableReadFilter \n"
+ "0 read(s) filtered by: GoodCigarReadFilter \n"
+ "0 total reads filtered";
+ "0 total reads filtered out of 0 reads processed";


final CountingReadFilter firstOfPair1AndMappingQuality0AndGoodCigar0 = firstOfPair1AndMappingQuality0.and(goodCigar0);
firstOfPair1AndMappingQuality0AndGoodCigar0.filteredCount = 1;
final CountingReadFilter firstOfPair1AndMappingQuality0AndGoodCigar0AndSecondOfPair2 = firstOfPair1AndMappingQuality0AndGoodCigar0.and(secondOfPair2);
final CountingReadFilter.CountingAndReadFilter firstOfPair1AndMappingQuality0AndGoodCigar0AndSecondOfPair2 = (CountingReadFilter.CountingAndReadFilter)firstOfPair1AndMappingQuality0AndGoodCigar0.and(secondOfPair2);
firstOfPair1AndMappingQuality0AndGoodCigar0AndSecondOfPair2.filteredCount = 3;
firstOfPair1AndMappingQuality0AndGoodCigar0AndSecondOfPair2.totalCount = 5;
final String multiAndWithMixCounts = "1 read(s) filtered by: FirstOfPairReadFilter \n"
+ "0 read(s) filtered by: MappingQualityAvailableReadFilter \n"
+ "0 read(s) filtered by: GoodCigarReadFilter \n"
+ "2 read(s) filtered by: SecondOfPairReadFilter \n"
+ "3 total reads filtered";
+ "3 total reads filtered out of 5 reads processed";

final CountingReadFilter firstOfPair1AndMappingQuality0AndGoodCigar0OrSecondOfPair2 = firstOfPair1AndMappingQuality0AndGoodCigar0.or(secondOfPair2);
firstOfPair1AndMappingQuality0AndGoodCigar0OrSecondOfPair2.filteredCount = 3;
Expand Down