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

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Dec 23, 2022
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updating the tests to reflect the new behavior around tracking total …
…reads on the and filter
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jamesemery committed Jul 19, 2022
commit 7791882a0c2b8afa838005bd1d8f2d9b4b1ca7f7
Original file line number Diff line number Diff line change
Expand Up @@ -201,7 +201,7 @@ public void resetFilteredCount() {
protected static final class CountingAndReadFilter extends CountingBinopReadFilter {

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

private CountingAndReadFilter(final CountingReadFilter lhs, final CountingReadFilter rhs) {
super(lhs, rhs);
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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;
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