add a couple piped input data tests

src/test/java/picard/sam/MergeBamAlignmentTest.java

@@ -75,8 +75,9 @@ public class MergeBamAlignmentTest extends CommandLineProgramTest {
     private static final File DATA_DIR = new File("testdata/picard/sam");
     private static final File TEST_DATA_DIR = new File(DATA_DIR, "MergeBamAlignment");
 
-    private static final File unmappedBam = new File(DATA_DIR, "unmapped.sam");
+    public static final File unmappedBam = new File(DATA_DIR, "unmapped.sam");
     private static final File alignedBam = new File(DATA_DIR, "aligned.sam");
+    public static final File alignedQuerySortedBam = new File(DATA_DIR, "aligned_query_name_sorted.sam");
     private static final File oneHalfAlignedBam = new File(DATA_DIR, "onehalfaligned.sam");
     private static final File otherHalfAlignedBam = new File(DATA_DIR, "otherhalfaligned.sam");
     private static final File mergingUnmappedBam = new File(TEST_DATA_DIR, "unmapped.sam");
@@ -87,8 +88,8 @@ public class MergeBamAlignmentTest extends CommandLineProgramTest {
     private static final File secondReadAlignedBam_firstHalf = new File(TEST_DATA_DIR, "firsthalf.read2.trimmed.aligned.sam");
     private static final File secondReadAlignedBam_secondHalf = new File(TEST_DATA_DIR, "secondhalf.read2.trimmed.aligned.sam");
     private static final File supplementalReadAlignedBam = new File(TEST_DATA_DIR, "aligned.supplement.sam");
-    private static final File alignedQuerynameSortedBam = new File(DATA_DIR, "aligned_queryname_sorted.sam");
-    private static final File fasta = new File(DATA_DIR, "merger.fasta");
+    public static final File alignedQuerynameSortedBam = new File(DATA_DIR, "aligned_queryname_sorted.sam");
+    public static final File fasta = new File(DATA_DIR, "merger.fasta");
     private static final String bigSequenceName = "chr7"; // The longest sequence in merger.fasta
     private static final File sequenceDict = new File(DATA_DIR, "merger.dict");
     private static final File sequenceDict2 = new File(DATA_DIR, "merger.2.dict");

src/test/java/picard/sam/PipedDataTest.java

@@ -1,44 +1,96 @@
 package picard.sam;
 
 import org.testng.Assert;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
-import picard.cmdline.CommandLineProgramTest;
+
+import java.io.File;
+import java.io.IOException;
+
+import static picard.sam.MergeBamAlignmentTest.fasta;
+import static picard.sam.MergeBamAlignmentTest.unmappedBam;
 
 public class PipedDataTest {
+    private final String classPath = "\"" + System.getProperty("java.class.path") + "\" ";
+    private final String picardCommandlinePreamble = "java -classpath " + classPath + "picard.cmdline.PicardCommandLine ";
 
-    private String classPath = "\"" + System.getProperty("java.class.path") + "\" ";
+    /**
+     * Creates the command line argument to be used for piped (/dev/stdin) input tests.
+     *
+     * @param inputSAM the path to the input SAM file.
+     * @return commandline for ViewSam.
+     */
+    private String getViewSamPicardCommand(final String inputSAM){
+        return picardCommandlinePreamble +
+                "ViewSam " +
+                "I=" + inputSAM + " " +
+                "ALIGNMENT_STATUS=All " +
+                "PF_STATUS=All ";
+    }
 
-    @Test
-    public void testSortSam() {
-        String[] command = {
+    @DataProvider(name = "pipedInputTestData")
+    public Object[][] getPipedInputTestData() throws IOException {
+        // Note the trailing space in each string block.
+        // TODO: port ArgumentBuilder from GATK so this would not be necessary.
+        final String[] sortSamCommand = {
                 "/bin/bash",
                 "-c",
-                "java -classpath " +
-                        classPath +
-                        "picard.cmdline.PicardCommandLine " +
-                        "ViewSam " +
-                        "I=testdata/picard/sam/test.bam " +
-                        "ALIGNMENT_STATUS=All " +
-                        "PF_STATUS=All " +
-                        "| " +
-                        "java -classpath " +
-                        classPath +
-                        "picard.cmdline.PicardCommandLine " +
-                        "SortSam " +
-                        "I=/dev/stdin " +
-                        "O=/dev/null " +
-                        "SORT_ORDER=queryname"
+                getViewSamPicardCommand("testdata/picard/sam/test.bam") +
+                "| " +
+                picardCommandlinePreamble +
+                "SortSam " +
+                "I=/dev/stdin " +
+                "O=/dev/null " +
+                "SORT_ORDER=queryname"
         };
 
+        final File temp = File.createTempFile("test", "sam");
+        temp.deleteOnExit();
+        final String[] revertSamCommand = {
+            "/bin/bash",
+            "-c",
+            getViewSamPicardCommand("testdata/picard/sam/test.bam") + // tsato: this has to be a "+", not ",". Best to extract a method "piped input argument builder" or something
+            "| " +
+            picardCommandlinePreamble +
+            "RevertSam " +
+            "I=/dev/stdin " +
+            "O=/dev/null "
+        };
+
+        // Only test the case where the "alignedBam" argument is /dev/stdin, which is the standard use case (bwa -> mergebamalignment)
+        // Make sure that the input aligned bam is query-name sorted (as it would be if it's piped from bwa)
+        // MergeBamAlignment fails if the coordinate sorted aligned bam is given, after trying to query-name sort dynamically and failing to find the reference header items,
+        // due seemingly to the fact that the input is /dev/stdin.
+        final String[] mergeBamAlignmentCommand = {
+                "/bin/bash",
+                "-c",
+                getViewSamPicardCommand(MergeBamAlignmentTest.alignedQuerynameSortedBam.getAbsolutePath()) + // here we have to use "+", not ",". Best to extract a method "piped input argument builder" or something
+                "| " +
+                picardCommandlinePreamble +
+                "MergeBamAlignment " +
+                "ALIGNED_BAM=/dev/stdin " +
+                "UNMAPPED=" + unmappedBam + " " +
+                "REFERENCE_SEQUENCE=" + fasta + " " +
+                "OUTPUT=/dev/null "
+        };
+
+        return new Object[][]{
+                {sortSamCommand},
+                {revertSamCommand},
+                {mergeBamAlignmentCommand}
+        };
+    }
+
+    @Test(dataProvider = "pipedInputTestData")
+    public void testPipedInput(final String[] command) {
         try {
             ProcessBuilder processBuilder = new ProcessBuilder(command);
             processBuilder.inheritIO();
 
             Process process = processBuilder.start();
             Assert.assertEquals(process.waitFor(), 0);
-
         } catch (Exception e) {
-            Assert.fail("Failed to pipe data from htsjdk to picard", e);
+            Assert.fail("Failed to pipe data to picard. The error was: ", e);
         }
     }
 }