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Description: some pieces of syntax are for OpenJDK-21, which is not yet the
default one in Debian. Let's remove this patch when it is.
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2024-04-21
--- a/src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/DataProcessorUtils.java
+++ b/src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/DataProcessorUtils.java
@@ -140,7 +140,7 @@
finalLF = AnnotationUtils.getInstance().getLocusFunction(lf, false);
}
// any instance of list l is fine.
- FunctionalData result = new FunctionalData(l.getFirst().getGene(), l.getFirst().getGeneStrand(), finalLF, l.getFirst().getReadStrand());
+ FunctionalData result = new FunctionalData(l.get(0).getGene(), l.get(0).getGeneStrand(), finalLF, l.get(0).getReadStrand());
resultList.add(result);
}
return (resultList);
--- a/src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/DropSeqPriorityScore.java
+++ b/src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/DropSeqPriorityScore.java
@@ -4,14 +4,20 @@
public class DropSeqPriorityScore implements PriorityScoreI {
public int getScore(FunctionalData fd) {
- int result = switch (fd.getLocusFunction()) {
- case null -> Integer.MAX_VALUE;
- case LocusFunction.CODING -> 1;
- case LocusFunction.UTR -> 1;
- case LocusFunction.INTRONIC -> 2;
- case LocusFunction.INTERGENIC -> 3;
- default -> Integer.MAX_VALUE;
- };
+ int result;
+ if (fd.getLocusFunction() == null) {
+ result = Integer.MAX_VALUE;
+ } else if (fd.getLocusFunction() == LocusFunction.CODING) {
+ result = 1;
+ } else if (fd.getLocusFunction() == LocusFunction.UTR) {
+ result = 1;
+ } else if (fd.getLocusFunction() == LocusFunction.INTRONIC) {
+ result = 2;
+ } else if (fd.getLocusFunction() == LocusFunction.INTERGENIC) {
+ result = 3;
+ } else {
+ result = Integer.MAX_VALUE;
+ }
return result;
}
--- a/src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/disambiguate/ClassifyDropSeqFunctionalData.java
+++ b/src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/disambiguate/ClassifyDropSeqFunctionalData.java
@@ -130,7 +130,7 @@
// simplify multiple annotations on the same gene.
if (filtered.isEmpty() && antisense.size()==1) {
- return antisense.getFirst();
+ return antisense.get(0);
}
return null;
}
@@ -145,7 +145,7 @@
List<FunctionalData> filtered = filterFunctionalData (fdList);
List<FunctionalData> sense = filtered.stream().filter(FunctionalData::isSense).toList();
if (sense.size()==1) {
- return sense.getFirst();
+ return sense.get(0);
}
return null;
}
--- a/src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/disambiguate/OptimusDropSeqLocusFunctionComparison.java
+++ b/src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/disambiguate/OptimusDropSeqLocusFunctionComparison.java
@@ -127,8 +127,8 @@
if (recs.size()<2)
continue;
- String cellBarcode = recs.getFirst().getStringAttribute(this.CELL_BARCODE_TAG);
- String umiBarcode = recs.getFirst().getStringAttribute(this.MOLECULAR_BARCODE_TAG);
+ String cellBarcode = recs.get(0).getStringAttribute(this.CELL_BARCODE_TAG);
+ String umiBarcode = recs.get(0).getStringAttribute(this.MOLECULAR_BARCODE_TAG);
Map<String, List<FunctionalData>> dropSeqFD = getFunctionalAnnotations(recs);
--- a/src/java/org/broadinstitute/dropseqrna/beadsynthesis/CorrectAndSplitScrnaReadPairs.java
+++ b/src/java/org/broadinstitute/dropseqrna/beadsynthesis/CorrectAndSplitScrnaReadPairs.java
@@ -171,7 +171,7 @@
}
++metrics.NUM_READS_CORRECTED_SINGLE_ED1;
numCandidatesHist.increment(1);
- return ed1Matches.getFirst();
+ return ed1Matches.get(0);
} else {
String bestBarcode = null;
double bestBarcodeLikelihood = 0;
--- a/src/java/org/broadinstitute/dropseqrna/beadsynthesis/CountBarcodeSequences.java
+++ b/src/java/org/broadinstitute/dropseqrna/beadsynthesis/CountBarcodeSequences.java
@@ -115,7 +115,7 @@
final SamReaderFactory readerFactory = SamReaderFactory.makeDefault();
final List<SamReader> readers = INPUT.stream().map(readerFactory::open).toList();
// Header is not important, but we need one to iterate
- final SAMFileHeader header = readers.getFirst().getFileHeader();
+ final SAMFileHeader header = readers.get(0).getFileHeader();
final CloseableIterator<SAMRecord> it = new UnsortedMergingSamRecordIterator(header, readers);
final Histogram<String> histogram = new Histogram<>("SEQUENCE", "COUNT");
--- a/src/java/org/broadinstitute/dropseqrna/utils/readiterators/GeneFunctionProcessor.java
+++ b/src/java/org/broadinstitute/dropseqrna/utils/readiterators/GeneFunctionProcessor.java
@@ -63,7 +63,7 @@
// If there's only one functional data result, re-tag the read, and
// queue it, then short circuit out.
if (fdList.size() == 1) {
- FunctionalData fd = fdList.getFirst();
+ FunctionalData fd = fdList.get(0);
SAMRecord rr = assignTagsToRead(r, fd);
result.add(rr);
return result;
@@ -114,11 +114,11 @@
// }
// test if all functional annotations are the same as the first entry.
- FunctionalData first = fdList.getFirst();
+ FunctionalData first = fdList.get(0);
boolean allSame = fdList.stream().allMatch(first::sameGeneAndType);
// if so, assign and finish.
if (allSame)
- return (assignTagsToRead(recs.getFirst(), first));
+ return (assignTagsToRead(recs.get(0), first));
return null;
}
--- a/src/java/org/broadinstitute/dropseqrna/utils/readiterators/SamFileMergeUtil.java
+++ b/src/java/org/broadinstitute/dropseqrna/utils/readiterators/SamFileMergeUtil.java
@@ -68,14 +68,14 @@
inputSortOrder = header.getSortOrder();
} else if (header.getSortOrder() != inputSortOrder) {
throw new PicardException(String.format("Sort order(%s) of %s does not agree with sort order(%s) of %s",
- header.getSortOrder(), inFile.getAbsolutePath(), inputSortOrder, inputs.getFirst().getAbsolutePath()));
+ header.getSortOrder(), inFile.getAbsolutePath(), inputSortOrder, inputs.get(0).getAbsolutePath()));
}
}
headers.add(header);
}
if (inputs.size() == 1) {
- return new SamHeaderAndIterator(headers.getFirst(), readers.getFirst().iterator());
+ return new SamHeaderAndIterator(headers.get(0), readers.get(0).iterator());
} else {
final SAMFileHeader.SortOrder outputSortOrder;
if (maintainSort) {
@@ -132,4 +132,4 @@
}
return new SamHeaderAndIterator(headerMerger.getMergedHeader(), iterator);
}
-}
\ No newline at end of file
+}
--- a/src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/StarSoloPriorityScore.java
+++ b/src/java/org/broadinstitute/dropseqrna/annotation/functionaldata/StarSoloPriorityScore.java
@@ -8,13 +8,18 @@
public class StarSoloPriorityScore implements PriorityScoreI {
public int getScore(FunctionalData fd) {
- int result = switch (fd.getLocusFunction()) {
- case LocusFunction.CODING -> 1;
- case LocusFunction.UTR -> 1;
- case LocusFunction.INTRONIC -> 2;
- case LocusFunction.INTERGENIC -> 3;
- default -> Integer.MAX_VALUE;
- };
+ int result;
+ if (fd.getLocusFunction() == LocusFunction.CODING) {
+ result = 1;
+ } else if (fd.getLocusFunction() == LocusFunction.UTR) {
+ result = 1;
+ } else if (fd.getLocusFunction() == LocusFunction.INTRONIC) {
+ result = 2;
+ } else if (fd.getLocusFunction() == LocusFunction.INTERGENIC) {
+ result = 3;
+ } else {
+ result = Integer.MAX_VALUE;
+ }
return result;
}
--- a/src/tests/java/org/broadinstitute/dropseqrna/annotation/functionaldata/DropSeqFunctionalDataProcessorTest.java
+++ b/src/tests/java/org/broadinstitute/dropseqrna/annotation/functionaldata/DropSeqFunctionalDataProcessorTest.java
@@ -84,7 +84,7 @@
// SENSE STRAND TEST positive strand
List<FunctionalData> fdList = fdp.getFilteredFunctionalData(genes, strands, locusFunctions, false);
Assert.assertEquals(fdList.size(), 1);
- FunctionalData fd = fdList.getFirst();
+ FunctionalData fd = fdList.get(0);
Assert.assertEquals(fd.getGene(), genes[0]);
Assert.assertEquals(fd.getGeneStrand(), strands[0]);
Assert.assertEquals(fd.getLocusFunction(), locusFunctions[0]);
@@ -136,7 +136,7 @@
List<FunctionalData> fdList = fdp.getFilteredFunctionalData(genes, strands, locusFunctions, false);
Assert.assertEquals(fdList.size(), 1);
- FunctionalData fd = fdList.getFirst();
+ FunctionalData fd = fdList.get(0);
Assert.assertEquals(fd.getGene(), genes[0]);
Assert.assertEquals(fd.getGeneStrand(), strands[0]);
Assert.assertEquals(fd.getLocusFunction(), locusFunctions[0]);
--- a/src/tests/java/org/broadinstitute/dropseqrna/annotation/functionaldata/StarSoloFunctionalDataProcessorTest.java
+++ b/src/tests/java/org/broadinstitute/dropseqrna/annotation/functionaldata/StarSoloFunctionalDataProcessorTest.java
@@ -82,7 +82,7 @@
// SENSE STRAND TEST positive strand
List<FunctionalData> fdList = fdp.getFilteredFunctionalData(genes, strands, locusFunctions, false);
Assert.assertEquals(fdList.size(), 2);
- FunctionalData fd = fdList.getFirst();
+ FunctionalData fd = fdList.get(0);
Assert.assertEquals(fd.getGene(), genes[0]);
Assert.assertEquals(fd.getGeneStrand(), strands[0]);
Assert.assertEquals(fd.getLocusFunction(), locusFunctions[0]);
@@ -134,7 +134,7 @@
List<FunctionalData> fdList = fdp.getFilteredFunctionalData(genes, strands, locusFunctions, false);
Assert.assertEquals(fdList.size(), 1);
- FunctionalData fd = fdList.getFirst();
+ FunctionalData fd = fdList.get(0);
Assert.assertEquals(fd.getGene(), genes[0]);
Assert.assertEquals(fd.getGeneStrand(), strands[0]);
Assert.assertEquals(fd.getLocusFunction(), locusFunctions[0]);
@@ -316,7 +316,7 @@
// once you filter to the preferred annotations, only the intronic gene is retained
fdList = fdp.filterToPreferredAnnotations(fdList);
Assert.assertEquals(fdList.size(), 1);
- Assert.assertEquals(fdList.getFirst().getGene(), "B");
+ Assert.assertEquals(fdList.get(0).getGene(), "B");
}
|
