Fix IOUtil.unrollPaths for http paths with query parameters (#1688)

* Stop treating query parameters in an http path as part of the file extension

src/main/java/htsjdk/samtools/util/IOUtil.java

@@ -1182,7 +1182,7 @@ public static List<Path> unrollPaths(final Collection<Path> inputs, final String
 
         while (!stack.empty()) {
             final Path p = stack.pop();
-            final String name = p.toString();
+            final String name = p.getFileName().toString();
             boolean matched = false;
 
             for (final String ext : extensions) {

src/test/java/htsjdk/samtools/util/IOUtilTest.java

@@ -450,6 +450,7 @@ public void testAssertDirectoryIsWritableFile(final File file, final boolean wri
 
     static final String level1 = "Level1.fofn";
     static final String level2 = "Level2.fofn";
+    static final String fofnHttpQueryParams = "FofnWithHttpQueryParams.fofn";
 
     @DataProvider
     public Object[][] fofnData() throws IOException {
@@ -460,11 +461,18 @@ public Object[][] fofnData() throws IOException {
         Path fofnPath2 = inMemoryFileSystem.getPath(level2);
         Files.copy(TEST_DATA_DIR.resolve(level2), fofnPath2);
 
+        Path withHttpPath = inMemoryFileSystem.getPath(fofnHttpQueryParams);
+        Files.copy(TEST_DATA_DIR.resolve(fofnHttpQueryParams), withHttpPath);
+
         return new Object[][]{
                 {TEST_DATA_DIR + "/" + level1, new String[]{".vcf", ".vcf.gz"}, 2},
                 {TEST_DATA_DIR + "/" + level2, new String[]{".vcf", ".vcf.gz"}, 4},
                 {fofnPath1.toUri().toString(), new String[]{".vcf", ".vcf.gz"}, 2},
-                {fofnPath2.toUri().toString(), new String[]{".vcf", ".vcf.gz"}, 4}
+                {fofnPath2.toUri().toString(), new String[]{".vcf", ".vcf.gz"}, 4},
+                //test http links with query parameters are handled correctly
+                //test disabled until NIO http provider is integrated
+                //see https://github.com/samtools/htsjdk/issues/1689
+                //{withHttpPath.toUri().toString(), new String[]{".vcf", ".vcf.gz"}, 4}
         };
     }
 

src/test/resources/htsjdk/samtools/io/FofnWithHttpQueryParams.fofn

@@ -0,0 +1,3 @@
+src/test/resources/htsjdk/samtools/io/Level1.fofn
+http://www.example.com/blurg.vcf
+http://www.example.com/blurg.vcf?huh=bleep,bloop