PrintHeader: a new tool to print a BAM header to a file

src/main/java/org/broadinstitute/hellbender/tools/PrintHeader.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 PrintHeader 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 bam header to " + outputFile, e);
+        }
+
+        logger.info("Successfully wrote BAM header to destination " + outputFile);
+    }
+}