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 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 filtered = filterFunctionalData (fdList); List 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> 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 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 it = new UnsortedMergingSamRecordIterator(header, readers); final Histogram 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 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 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 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 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"); }