Excise SRA support and ngs-java dependency

README.md

@@ -96,7 +96,6 @@ Broadly speaking the majority of the code is covered under the MIT license with
 
 * Much of the CRAM code is under the Apache License, Version 2
 * Core `tribble` code (underlying VCF reading/writing amongst other things) is under LGPL
-* Code supporting the reading/writing of SRA format is uncopyrighted & public domain
 
 ### Java Minimum Version Support Policy
 

build.gradle

@@ -51,7 +51,6 @@ dependencies {
     implementation "org.json:json:20231013"
     implementation 'org.openjdk.nashorn:nashorn-core:15.4'
 
-    api "gov.nih.nlm.ncbi:ngs-java:2.9.0"
     api "org.apache.commons:commons-jexl:2.1.1"
 
     testImplementation 'org.testng:testng:7.8.0'
@@ -225,13 +224,13 @@ tasks.register('testWithOptimisticVCF4_4', Test) {
 }
 
 test {
-    description = "Runs the unit tests other than the SRA tests"
+    description = "Runs the unit tests other than external-API tests"
 
    useTestNG {
        if (OperatingSystem.current().isUnix()) {
-           excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_4", "ftp", "http", "sra", "ena", "htsget"
+           excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_4", "ftp", "http", "ena", "htsget"
        } else {
-           excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_4", "ftp", "http", "sra", "ena", "htsget", "unix"
+           excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_4", "ftp", "http", "ena", "htsget", "unix"
        }
        parallel = "classes"
        threadCount = Runtime.runtime.availableProcessors()
@@ -250,13 +249,12 @@ tasks.register('testFTP', Test) {
 }
 
 tasks.register('testExternalApis', Test) {
-    description = "Run the SRA, ENA, and HTTP tests (tests that interact with external APIs)"
+    description = "Run the 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 {
-        includeGroups "sra", "http", "ena"
+        includeGroups "http", "ena"
         excludeGroups "slow", "broken"
     }
 }

src/main/java/htsjdk/beta/plugin/reads/ReadsBundle.java

@@ -201,7 +201,7 @@ private static <T extends IOPath> Optional<Tuple<String, String>> getInferredCon
             } else if (ext.equals((FileExtensions.SAM))) {
                 return Optional.of(new Tuple<>(BundleResourceType.CT_ALIGNED_READS, BundleResourceType.FMT_READS_SAM));
             }
-            // TODO: finish this, else SRA, htsget,...
+            // TODO: finish this, else htsget,...
         }
         return Optional.empty();
     }

src/main/java/htsjdk/samtools/Defaults.java

@@ -95,12 +95,6 @@ public class Defaults {
      */
     public static final String EBI_REFERENCE_SERVICE_URL_MASK;
 
-    /**
-     * Boolean describing whether downloading of SRA native libraries is allowed,
-     * in case such native libraries are not found locally.  Default = false.
-     */
-    public static final boolean SRA_LIBRARIES_DOWNLOAD;
-
     /**
      * Whether to attempt to use jlibdeflate (libdeflate via JNI) for DEFLATE compression and decompression.
      * When true, the default deflater/inflater factories will try to load the native library and fall back
@@ -143,7 +137,6 @@ public class Defaults {
         CUSTOM_READER_FACTORY = getStringProperty("custom_reader", "");
         SAM_FLAG_FIELD_FORMAT =
                 SamFlagField.valueOf(getStringProperty("sam_flag_field_format", SamFlagField.DECIMAL.name()));
-        SRA_LIBRARIES_DOWNLOAD = getBooleanProperty("sra_libraries_download", false);
         USE_LIBDEFLATE = getBooleanProperty("use_libdeflate", true);
         DISABLE_SNAPPY_COMPRESSOR = getBooleanProperty(DISABLE_SNAPPY_PROPERTY_NAME, false);
         OPTIMISTIC_VCF_4_4 = getBooleanProperty(OPTIMISTIC_VCF_4_4_PROPERTY, false);