PrintReadsHeader: a new tool to print a BAM/SAM/CRAM header to a file (…

…#6153)

* PrintReadsHeader: a new tool to print a BAM/SAM/CRAM header to a file

* Added an integration test for PrintReadsHeader

src/main/java/org/broadinstitute/hellbender/tools/PrintReadsHeader.java

@@ -0,0 +1,45 @@
+package org.broadinstitute.hellbender.tools;
+
+import htsjdk.samtools.SAMFileHeader;
+import htsjdk.samtools.SAMTextHeaderCodec;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.engine.GATKTool;
+import org.broadinstitute.hellbender.exceptions.UserException;
+import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
+
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+
+@CommandLineProgramProperties(
+        summary = "Prints the header from the input SAM/BAM/CRAM file to a textual output file",
+        oneLineSummary = "Print the header from a SAM/BAM/CRAM file",
+        programGroup = ReadDataManipulationProgramGroup.class
+)
+@DocumentedFeature
+public class PrintReadsHeader extends GATKTool {
+
+    @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc = "file to write the bam header to", optional = false)
+    private String outputFile;
+
+    @Override
+    public boolean requiresReads() {
+        return true;
+    }
+
+    @Override
+    public void traverse() {
+        final SAMFileHeader bamHeader = getHeaderForReads();
+
+        try ( final PrintWriter outputWriter = new PrintWriter(outputFile) ) {
+            final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
+            codec.encode(outputWriter, bamHeader);
+        } catch (FileNotFoundException e ) {
+            throw new UserException.CouldNotCreateOutputFile("Error writing reads header to " + outputFile, e);
+        }
+
+        logger.info("Successfully wrote reads header to destination: " + outputFile);
+    }
+}

src/test/java/org/broadinstitute/hellbender/tools/PrintReadsHeaderIntegrationTest.java

@@ -0,0 +1,27 @@
+package org.broadinstitute.hellbender.tools;
+
+import org.broadinstitute.hellbender.CommandLineProgramTest;
+import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+
+public final class PrintReadsHeaderIntegrationTest extends CommandLineProgramTest {
+
+    private static final File TEST_DATA_DIR = getTestDataDir();
+
+    @Test
+    public void testPrintReadsHeader() throws IOException {
+        final File inFile = new File(TEST_DATA_DIR, "print_reads.sorted.bam");
+        final File outFile = createTempFile("PrintReadsHeaderIntegrationTest_testPrintBAMHeader", ".txt");
+        final String[] args = new String[] {
+                "--input" , inFile.getAbsolutePath(),
+                "--output", outFile.getAbsolutePath()
+        };
+        runCommandLine(args);
+
+        //Make sure contents are the same
+        IntegrationTestSpec.assertEqualTextFiles(outFile, new File(TEST_DATA_DIR, "print_reads.sorted.bam.header.txt"));
+    }
+}

src/test/resources/org/broadinstitute/hellbender/tools/print_reads.sorted.bam.header.txt

@@ -0,0 +1,11 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr2	LN:101
+@SQ	SN:chr3	LN:101
+@SQ	SN:chr4	LN:101
+@SQ	SN:chr5	LN:101
+@SQ	SN:chr6	LN:101
+@SQ	SN:chr7	LN:454
+@SQ	SN:chr8	LN:202
+@RG	ID:0	SM:Hi,Mom!	PL:ILLUMINA
+@PG	ID:1	VN:2.0	PN:Hey!