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Fix existing deprecations in code and build. #1767

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Merged
tfenne merged 1 commit into from
Apr 11, 2026
Merged

Fix existing deprecations in code and build. #1767

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8 changes: 8 additions & 0 deletions build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -118,6 +118,8 @@ tasks.withType(Test).configureEach { task ->

tasks.register('testWithDefaultReference', Test) {
description = "Run tests with a default reference File"
testClassesDirs = sourceSets.test.output.classesDirs
classpath = sourceSets.test.runtimeClasspath
jvmArgs += '-Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa'

useTestNG {
Expand All @@ -127,6 +129,8 @@ tasks.register('testWithDefaultReference', Test) {

tasks.register('testWithOptimisticVCF4_4', Test) {
description = "Run tests with optimistic VCF 4.4 reading"
testClassesDirs = sourceSets.test.output.classesDirs
classpath = sourceSets.test.runtimeClasspath
jvmArgs += '-Dsamjdk.optimistic_vcf_4_4=true'

useTestNG {
Expand All @@ -151,6 +155,8 @@ test {

tasks.register('testFTP', Test) {
description = "Runs the tests that require connection to a remote ftp server"
testClassesDirs = sourceSets.test.output.classesDirs
classpath = sourceSets.test.runtimeClasspath
useTestNG {
includeGroups "ftp"
excludeGroups "slow", "broken"
Expand All @@ -159,6 +165,8 @@ tasks.register('testFTP', Test) {

tasks.register('testExternalApis', Test) {
description = "Run the SRA, ENA, and HTTP tests (tests that interact with external APIs)"
testClassesDirs = sourceSets.test.output.classesDirs
classpath = sourceSets.test.runtimeClasspath
jvmArgs += '-Dsamjdk.sra_libraries_download=true'

useTestNG {
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54 changes: 27 additions & 27 deletions src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java
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Expand Up @@ -12,18 +12,18 @@ public class SAMBinaryTagAndValueUnitTest extends HtsjdkTest {
public Object[][] allowedTypes() {
return new Object[][] {
{new String("a string")},
{new Byte((byte) 7)},
{new Short((short) 8)},
{new Integer(0)},
{new Character('C')},
{new Float(0.1F)},
{Byte.valueOf((byte) 7)},
{Short.valueOf((short) 8)},
{Integer.valueOf(0)},
{Character.valueOf('C')},
{Float.valueOf(0.1F)},
// unsigned longs
{new Long(0)},
{new Long(BinaryCodec.MAX_UINT)},
{Long.valueOf(0)},
{Long.valueOf(BinaryCodec.MAX_UINT)},
// signed longs
{new Long(-1L)},
{new Long(Integer.MAX_VALUE)},
{new Long(Integer.MIN_VALUE)},
{Long.valueOf(-1L)},
{Long.valueOf(Integer.MAX_VALUE)},
{Long.valueOf(Integer.MIN_VALUE)},
// array values
{new byte[]{0, 1, 2}},
{new short[]{3, 4, 5}},
Expand All @@ -45,9 +45,9 @@ public void test_isAllowedConstructor(final Object value) {
@DataProvider(name="notAllowedAttributeTypes")
public Object[][] notAllowedTypes() {
return new Object[][] {
{new Long(BinaryCodec.MAX_UINT + 1L)},
{new Long(Integer.MIN_VALUE - 1L)},
{new Double(0.3F)},
{Long.valueOf(BinaryCodec.MAX_UINT + 1L)},
{Long.valueOf(Integer.MIN_VALUE - 1L)},
{Double.valueOf(0.3F)},
{new Object()},
{new Object[]{}},
{new Integer[]{}}
Expand Down Expand Up @@ -100,26 +100,26 @@ public Object[][] hashCopyEquals() {
{new SAMBinaryTagAndValue(tag, new String("a string")), new SAMBinaryTagAndValue(tag, new String("a string")), true, true},
{new SAMBinaryTagAndValue(tag, new String("a string")), new SAMBinaryTagAndValue(tag, new String("different string")), false, false},

{new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), true, true},
{new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 1)), false, false},
{new SAMBinaryTagAndValue(tag, Byte.valueOf((byte) 0)), new SAMBinaryTagAndValue(tag, Byte.valueOf((byte) 0)), true, true},
{new SAMBinaryTagAndValue(tag, Byte.valueOf((byte) 0)), new SAMBinaryTagAndValue(tag, Byte.valueOf((byte) 1)), false, false},

{new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 0)), true, true},
{new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 1)), false, false},
{new SAMBinaryTagAndValue(tag, Short.valueOf((short) 0)), new SAMBinaryTagAndValue(tag, Short.valueOf((short) 0)), true, true},
{new SAMBinaryTagAndValue(tag, Short.valueOf((short) 0)), new SAMBinaryTagAndValue(tag, Short.valueOf((short) 1)), false, false},

{new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
{new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
{new SAMBinaryTagAndValue(tag, Integer.valueOf(0)), new SAMBinaryTagAndValue(tag, Integer.valueOf(0)), true, true},
{new SAMBinaryTagAndValue(tag, Integer.valueOf(0)), new SAMBinaryTagAndValue(tag, Integer.valueOf(0)), true, true},

{new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('C')), true, true},
{new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('D')), false, false},
{new SAMBinaryTagAndValue(tag, Character.valueOf('C')), new SAMBinaryTagAndValue(tag, Character.valueOf('C')), true, true},
{new SAMBinaryTagAndValue(tag, Character.valueOf('C')), new SAMBinaryTagAndValue(tag, Character.valueOf('D')), false, false},

{new SAMBinaryTagAndValue(tag,new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.1F)), true, true},
{new SAMBinaryTagAndValue(tag, new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.2F)), false, false},
{new SAMBinaryTagAndValue(tag,Float.valueOf(0.1F)), new SAMBinaryTagAndValue(tag, Float.valueOf(0.1F)), true, true},
{new SAMBinaryTagAndValue(tag, Float.valueOf(0.1F)), new SAMBinaryTagAndValue(tag, Float.valueOf(0.2F)), false, false},

{new SAMBinaryTagAndValue(tag,new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(37L)), true, true},
{new SAMBinaryTagAndValue(tag, new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(38L)), false, false},
{new SAMBinaryTagAndValue(tag,Long.valueOf(37L)), new SAMBinaryTagAndValue(tag, Long.valueOf(37L)), true, true},
{new SAMBinaryTagAndValue(tag, Long.valueOf(37L)), new SAMBinaryTagAndValue(tag, Long.valueOf(38L)), false, false},

{new SAMBinaryTagAndValue(tag,new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), true, true},
{new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT-1)), false, false},
{new SAMBinaryTagAndValue(tag,Long.valueOf(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, Long.valueOf(BinaryCodec.MAX_UINT)), true, true},
{new SAMBinaryTagAndValue(tag, Long.valueOf(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, Long.valueOf(BinaryCodec.MAX_UINT-1)), false, false},

// arrays

Expand Down
2 changes: 1 addition & 1 deletion src/test/java/htsjdk/samtools/SAMTextWriterTest.java
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Expand Up @@ -85,7 +85,7 @@ private void doTest(final SAMRecordSetBuilder recordSetBuilder, final SamFlagFie
final File samFile = File.createTempFile("tmp.", ".sam");
samFile.deleteOnExit();
final Map<String, Object> tagMap = new HashMap<String, Object>();
tagMap.put("XC", new Character('q'));
tagMap.put("XC", 'q');
tagMap.put("XI", 12345);
tagMap.put("XF", 1.2345f);
tagMap.put("XS", "Hi,Mom!");
Expand Down
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