Description: using the correct SamReader api Author: Pierre Gruet Origin: https://sources.debian.org/src/fastqc/0.11.9+dfsg-4/debian/patches/htsjdk-api.patch Forwarded: not-needed Last-Update: 2020-11-06 --- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java +++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java @@ -32,9 +32,7 @@ import org.campagnelab.goby.util.dynoptions.RegisterThis; import htsjdk.samtools.ValidationStringency; import it.unimi.dsi.logging.ProgressLogger; -import htsjdk.samtools.SAMFileReader; -import htsjdk.samtools.SAMRecord; -import htsjdk.samtools.SAMRecordIterator; +import htsjdk.samtools.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -284,12 +282,15 @@ } System.out.println("Comparing source bam and destination bam"); - final SAMFileReader sourceParser = new SAMFileReader(new FileInputStream(sourceBamFile)); - final SAMFileReader destParser = new SAMFileReader(new FileInputStream(destBamFile)); + final SamInputResource sirSource = SamInputResource.of(new FileInputStream(sourceBamFile)); + final SamReaderFactory srfSource = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + final SamInputResource sirDest = SamInputResource.of(new FileInputStream(destBamFile)); + final SamReaderFactory srfDest = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader sourceParser = srfSource.open(sirSource); + final SamReader destParser = srfDest.open(sirDest); // We need to set the validation to silent because an incomplete file (if the source isn't the entire file) // we can see errors that wouldn't exist in a real conversion. - sourceParser.setValidationStringency(ValidationStringency.SILENT); - destParser.setValidationStringency(ValidationStringency.SILENT); final SAMRecordIterator sourceIterator = sourceParser.iterator(); final SAMRecordIterator destIterator = destParser.iterator(); AlignmentReaderImpl gobyReader = null; --- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactMode.java +++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactMode.java @@ -242,10 +242,11 @@ final ProgressLogger progress = new ProgressLogger(LOG); progress.displayFreeMemory = true; // the following is required to set validation to SILENT before loading the header (done in the SAMFileReader constructor) - SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT); - final InputStream stream = "-".equals(inputFile) ? System.in : new FileInputStream(inputFile); - final SAMFileReader parser = new SAMFileReader(stream); + final SamInputResource sir = SamInputResource.of(stream); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); // transfer read groups to Goby header: final SAMFileHeader samHeader = parser.getFileHeader(); final IndexedIdentifier readGroups = new IndexedIdentifier(); --- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactOldMode.java +++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactOldMode.java @@ -128,8 +128,10 @@ final int[] readLengths = createReadLengthArray(); final ProgressLogger progress = new ProgressLogger(LOG); - final SAMFileReader parser = new SAMFileReader(new File(inputFile)); - parser.setValidationStringency(ValidationStringency.SILENT); + final SamInputResource sir = SamInputResource.of(new File(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); progress.start(); --- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.java +++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.java @@ -231,10 +231,11 @@ final ProgressLogger progress = new ProgressLogger(LOG); progress.displayFreeMemory = true; // the following is required to set validation to SILENT before loading the header (done in the SAMFileReader constructor) - SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT); - final InputStream stream = "-".equals(inputFile) ? System.in : new FileInputStream(inputFile); - final SAMFileReader parser = new SAMFileReader(stream); + final SamInputResource sir = SamInputResource.of(stream); + SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); // transfer read groups to Goby header: final SAMFileHeader samHeader = parser.getFileHeader(); final IndexedIdentifier readGroups = new IndexedIdentifier(); @@ -827,4 +828,4 @@ } -} \ No newline at end of file +} --- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java +++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java @@ -30,8 +30,7 @@ import htsjdk.samtools.ValidationStringency; import it.unimi.dsi.lang.MutableString; import it.unimi.dsi.logging.ProgressLogger; -import htsjdk.samtools.SAMFileReader; -import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -142,8 +141,10 @@ try { final ProgressLogger progress = new ProgressLogger(LOG); // the following is required to set validation to SILENT before loading the header (done in the SAMFileReader constructor) - SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT); - final SAMFileReader parser = new SAMFileReader(new File(inputFilename), null); + final SamInputResource sir = SamInputResource.of(new File(inputFilename)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); progress.start(); --- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java +++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java @@ -29,8 +29,7 @@ import it.unimi.dsi.fastutil.ints.IntArrayList; import it.unimi.dsi.fastutil.ints.IntList; import it.unimi.dsi.lang.MutableString; -import htsjdk.samtools.SAMFileReader; -import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.*; import org.apache.commons.lang.ArrayUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -350,8 +349,10 @@ private int processSamReadsFile(final String inputFilename) throws IOException { // Create directory for output file if it doesn't already exist int i = 0; - SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT); - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFilename)); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFilename)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { final String quality = samRecord.getBaseQualityString(); if (quality != null && quality.length() != 0) { --- a/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/RoundTripAlignment.java +++ b/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/RoundTripAlignment.java @@ -32,9 +32,7 @@ import org.campagnelab.goby.reads.RandomAccessSequenceTestSupport; import htsjdk.samtools.ValidationStringency; import it.unimi.dsi.logging.ProgressLogger; -import htsjdk.samtools.SAMFileReader; -import htsjdk.samtools.SAMRecord; -import htsjdk.samtools.SAMRecordIterator; +import htsjdk.samtools.*; import org.apache.commons.io.FilenameUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -172,12 +170,15 @@ } LOG.info("Comparing source bam and destination bam"); - final SAMFileReader sourceParser = new SAMFileReader(new FileInputStream(sourceBamFilename)); - final SAMFileReader destParser = new SAMFileReader(new FileInputStream(destBamFilename)); + final SamInputResource sirSource = SamInputResource.of(new FileInputStream(sourceBamFilename)); + final SamReaderFactory srfSource = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + final SamInputResource sirDest = SamInputResource.of(new FileInputStream(destBamFilename)); + final SamReaderFactory srfDest = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader sourceParser = srfSource.open(sirSource); + final SamReader destParser = srfDest.open(sirDest); // We need to set the validation to silent because an incomplete file (if the source isn't the entire file) // we can see errors that wouldn't exist in a real conversion. - sourceParser.setValidationStringency(ValidationStringency.SILENT); - destParser.setValidationStringency(ValidationStringency.SILENT); final SAMRecordIterator sourceIterator = sourceParser.iterator(); final SAMRecordIterator destIterator = destParser.iterator(); AlignmentReaderImpl gobyReader = null; --- a/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/TestSamRecordParser.java +++ b/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/TestSamRecordParser.java @@ -25,8 +25,7 @@ import htsjdk.samtools.ValidationStringency; import it.unimi.dsi.lang.MutableString; import junit.framework.Assert; -import htsjdk.samtools.SAMFileReader; -import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.*; import org.apache.commons.io.FilenameUtils; import org.slf4j.Logger; import org.junit.BeforeClass; @@ -65,8 +64,10 @@ // like 9 no genome public void testSamToCompactTrickCase9NoGenome() throws IOException { final String inputFile = "test-data/splicedsamhelper/tricky-spliced-9.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); - parser.setValidationStringency(ValidationStringency.SILENT); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { @@ -84,8 +85,10 @@ public void testSamToCompactTrickCase10NoGenome() throws IOException { final String inputFile = "test-data/splicedsamhelper/tricky-spliced-10.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); - parser.setValidationStringency(ValidationStringency.SILENT); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { @@ -103,8 +106,10 @@ @Test public void testSamToCompactTrickCase11() throws IOException { final String inputFile = "test-data/splicedsamhelper/tricky-spliced-11.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); - parser.setValidationStringency(ValidationStringency.SILENT); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { @@ -121,8 +126,11 @@ public void testSamToCompactTrickCase12NoGenome() throws IOException { final String inputFile = "test-data/splicedsamhelper/tricky-spliced-12.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); final SamRecordParser recordParser = new SamRecordParser(); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { final GobySamRecord gobySamRecord = recordParser.processRead(samRecord); @@ -146,7 +154,10 @@ public void testSamToCompactTrickCase13NoGenomeSoftClips() throws IOException { final String inputFile = "test-data/splicedsamhelper/tricky-spliced-13.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { @@ -179,8 +190,10 @@ public void testSamToCompactTrickCase13SoftClipsWithGenome() throws IOException { final String inputFile = "test-data/splicedsamhelper/tricky-spliced-14.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); - parser.setValidationStringency(ValidationStringency.SILENT); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); @@ -209,7 +222,10 @@ public void testSamToCompactTrickCase15NoGenomeThreeSplice() throws IOException { final String inputFile = "test-data/splicedsamhelper/tricky-spliced-15.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { final GobySamRecord gobySamRecord = recordParser.processRead(samRecord); @@ -247,8 +263,10 @@ public void testSamToCompactTrickCase16() throws IOException { final String inputFile = "test-data/splicedsamhelper/tricky-spliced-16.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); - parser.setValidationStringency(ValidationStringency.SILENT); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { final GobySamRecord gobySamRecord = recordParser.processRead(samRecord); @@ -337,8 +355,10 @@ @Test public void testSamToCompactTrickCase17() throws IOException { final String inputFile = "test-data/splicedsamhelper/tricky-spliced-17.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); - parser.setValidationStringency(ValidationStringency.SILENT); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { final GobySamRecord gobySamRecord = recordParser.processRead(samRecord); @@ -422,8 +442,10 @@ @Test public void testDelNonSplice1() throws IOException { final String inputFile = "test-data/splicedsamhelper/del-nonsplice-1.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); - parser.setValidationStringency(ValidationStringency.SILENT); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { final GobySamRecord gobySamRecord = recordParser.processRead(samRecord); @@ -453,8 +475,10 @@ @Test public void testLeftPadding1() throws IOException { final String inputFile = "test-data/splicedsamhelper/leftpad-nosplice-1.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); - parser.setValidationStringency(ValidationStringency.SILENT); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) { final GobySamRecord gobySamRecord = recordParser.processRead(samRecord); @@ -491,8 +515,10 @@ @Test public void testSeqVarReads() throws IOException { final String inputFile = "test-data/seq-var-test/seq-var-reads-gsnap.sam"; - final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile)); - parser.setValidationStringency(ValidationStringency.SILENT); + final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile)); + final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); + + final SamReader parser = srf.open(sir); final SamRecordParser recordParser = new SamRecordParser(); final PositionToBasesMap seqvarDataMap = TestIteratedSortedAlignment2.readSeqVarFile( "test-data/seq-var-test/seq-var-reads-gsnap.seqvar");