Updated to Picard for BAMIndexer, BAMFileSort, and MergeSamFiles

.gitignore

@@ -3,3 +3,4 @@
 /.gradle/
 /build/
 .metadata
+.idea

src/main/java/scriptmanager/scripts/BAM_Manipulation/BAIIndexer.java

@@ -1,47 +1,42 @@
 package scriptmanager.scripts.BAM_Manipulation;
 
-import htsjdk.samtools.BAMIndexer;
-import htsjdk.samtools.SAMRecord;
-import htsjdk.samtools.SamReader;
-import htsjdk.samtools.SamReaderFactory;
-import htsjdk.samtools.ValidationStringency;
+import picard.sam.BuildBamIndex;
 
 import java.io.File;
 import java.io.IOException;
-import java.text.NumberFormat;
-
-import javax.swing.JOptionPane;
+import java.util.ArrayList;
 
+/**
+ * Picard wrapper for BuildBamIndex
+ * 
+ * @author Erik Pavloski
+ * @see scriptmanager.window_interface.BAM_Manipulation.BAIIndexerWIndow
+ */
 public class BAIIndexer {
+	/**
+	 * Index a BAM file and output said index to a file of the same name with a .bai
+	 * extension
+	 * 
+	 * @param input the BAM file to index
+	 * @return the BAM index file (.bai)
+	 * @throws IOException
+	 */
 	public static File generateIndex(File input) throws IOException {
-		SamReaderFactory factory = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS).validationStringency(ValidationStringency.LENIENT);
-		File retVal = null;
-		System.out.println("Generating New Index File...");
-		try{
-			String output = input.getCanonicalPath() + ".bai";
-			retVal = new File(output);
-			//Generate index
-			SamReader inputSam = factory.open(input);
-			BAMIndexer bamindex = new BAMIndexer(retVal, inputSam.getFileHeader());
-			int counter = 0;
-			for(SAMRecord record : inputSam) {
-				if(counter % 1000000 == 0) {
-					System.out.print("Tags processed: " + NumberFormat.getIntegerInstance().format(counter) + "\r");
-					System.out.flush();
-				}
-				counter++;
-				bamindex.processAlignment(record);
-			}
-			bamindex.finish();
-			inputSam.close();
-			System.out.println("\nIndex File Generated");
-			return retVal;
-		}
-		catch(htsjdk.samtools.SAMException exception){
-			System.out.println(exception.getMessage());
-			JOptionPane.showMessageDialog(null, exception.getMessage());
-			retVal = null;
-		}
+		// Tells user that their file is being generated
+		System.out.println("Generating Index File...");
+		// Build output filepath
+		String output = input.getCanonicalPath() + ".bai";
+		File retVal = new File(output);
+		// Instatiate Picard object
+		final BuildBamIndex buildBamIndex = new BuildBamIndex();
+		// Build input argument string
+		final ArrayList<String> args = new ArrayList<>();
+		args.add("INPUT=" + input.getAbsolutePath());
+		args.add("OUTPUT=" + retVal.getAbsolutePath());
+		// Call Picard with args
+		buildBamIndex.instanceMain(args.toArray(new String[args.size()]));
+
+		System.out.println("Index File Generated");
 		return retVal;
 	}
 }

src/main/java/scriptmanager/scripts/BAM_Manipulation/BAMFileSort.java

@@ -1,25 +1,39 @@
 package scriptmanager.scripts.BAM_Manipulation;
 
+import htsjdk.samtools.SAMException;
 import htsjdk.samtools.SAMFileHeader;
-import htsjdk.samtools.SAMFileWriter;
-import htsjdk.samtools.SAMFileWriterFactory;
-import htsjdk.samtools.SAMRecord;
-import htsjdk.samtools.SamReader;
-import htsjdk.samtools.SamReaderFactory;
-import htsjdk.samtools.util.IOUtil;
+import picard.sam.SortSam;
 
 import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
 
+/**
+ * Picard wrapper for MergeSamFiles SortSam
+ * 
+ * @author Erik Pavloski
+ * @see scriptmanager.window_interface.BAM_Manipulation.SortBAMWindow
+ */
 public class BAMFileSort {
-	public static void sort(File INPUT, File OUTPUT) {
-		IOUtil.assertFileIsReadable(INPUT);
-        IOUtil.assertFileIsWritable(OUTPUT);
-        final SamReader reader = SamReaderFactory.makeDefault().open(INPUT);
-        reader.getFileHeader().setSortOrder(SAMFileHeader.SortOrder.coordinate);
-        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), false, OUTPUT);
-        for (final SAMRecord rec: reader) {
-            writer.addAlignment(rec);
-        }
-        writer.close();
-	}
-}
+	/**
+	 * The following code uses Picard's SortSam to sort a BAM file by coordinate
+	 * 
+	 * @param input the BAM file to be sorted (corresponds to INPUT)
+	 * @param output the file to write the sorted BAM to (corresponds to OUTPUT)
+	 * @throws SAMException
+	 * @throws IOException
+	 */
+    public static void sort(File input, File output) throws SAMException, IOException {
+        // Tells user their File is being sorted
+        System.out.println("Sorting Bam File...");
+		// Instatiate Picard object
+            final SortSam sorter = new SortSam();
+		// Build input argument string
+            final ArrayList<String> args = new ArrayList<>();
+            args.add("INPUT=" + input.getAbsolutePath());
+            args.add("OUTPUT=" + output.getAbsolutePath());
+            args.add("SORT_ORDER=" + SAMFileHeader.SortOrder.coordinate);
+            // Call Picard with args
+            sorter.instanceMain(args.toArray(new String[args.size()]));
+    }
+}

src/main/java/scriptmanager/scripts/BAM_Manipulation/MergeBAM.java

@@ -0,0 +1,49 @@
+package scriptmanager.scripts.BAM_Manipulation;
+
+import htsjdk.samtools.SAMException;
+import picard.sam.MergeSamFiles;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+
+/**
+ * Picard wrapper for MergeSamFiles
+ * 
+ * @author Erik Pavloski
+ * @see scriptmanager.window_interface.BAM_Manipulation
+ */
+public class MergeBAM {
+	/**
+	 * Excecute the Picard MergeSamFiles command line tool after checking ever input file has been indexed.
+	 * 
+	 * @param inputs the list of input files to merge (corresponds to several INPUT values)
+	 * @param output the output file for the merged BAM file (corresponds to OUTPUT)
+	 * @param useMultipleCpus whether or not to parallelize (corresponds to USE_THREADING)
+	 * @throws SAMException
+	 * @throws IOException
+	 */
+	public static void run(ArrayList<File> inputs, File output, boolean useMultipleCpus) throws SAMException, IOException {
+		// Check all BAM files have an index
+		for (int x = 0; x<inputs.size(); x++) {
+			File f = new File(inputs.get(x) + ".bai");
+			if(!f.exists() || f.isDirectory()) {
+				throw new SAMException("BAI Index File does not exist for: " + inputs.get(x).getName() + "\n");
+			}
+		}
+		// Tells the user their files are being merged
+		System.out.println("Merging BAM Files...");
+		// Merges the files
+		final MergeSamFiles merger = new MergeSamFiles();
+		final ArrayList<String> args = new ArrayList<>();
+		for (File input : inputs) {
+			args.add("INPUT=" + input.getAbsolutePath());
+		}
+		args.add("OUTPUT=" + output.getAbsolutePath());
+		if (useMultipleCpus) {
+			args.add("USE_THREADING=true");
+		}
+		merger.instanceMain(args.toArray(new String[args.size()]));
+		System.out.println("BAM Files Merged.");
+	}
+}