Merge branch 'dev' into working-dev

.gitignore

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

src/main/java/scriptmanager/cli/BAM_Manipulation/BAMRemoveDupCLI.java

@@ -2,6 +2,7 @@
 
 import picocli.CommandLine.Command;
 
+import java.io.File;
 import java.util.concurrent.Callable;
 
 import scriptmanager.objects.ToolDescriptions;
@@ -29,4 +30,13 @@ public Integer call() throws Exception {
 		System.exit(1);
 		return(1);
 	}
+
+	public static String getCLIcommand(File BAM, boolean removeDuplicates, File OUTPUT, File METRICS) {
+		String command = "java -jar $PICARD MarkDuplicates";
+		command += " INPUT=" + BAM.getAbsolutePath();
+		command += " OUTPUT=" + OUTPUT.getAbsolutePath();
+		command += " METRICS_FILE=" + METRICS.getAbsolutePath();
+		command += removeDuplicates ? "REMOVE_DUPLICATES=true" : "REMOVE_DUPLICATES=false";
+		return(command);
+	}
 }

src/main/java/scriptmanager/cli/BAM_Statistics/CrossCorrelationCLI.java

@@ -0,0 +1,126 @@
+package scriptmanager.cli.BAM_Statistics;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.concurrent.Callable;
+
+import picocli.CommandLine.ArgGroup;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Parameters;
+import scriptmanager.objects.ToolDescriptions;
+import scriptmanager.objects.ArchTEx.CorrParameter;
+import scriptmanager.scripts.BAM_Statistics.CrossCorrelation;
+import scriptmanager.util.ExtensionFileFilter;
+
+/**
+ * Command line interface class for performing the ArchTEX cross correlation
+ * analysis by calling a method implemented in the scripts package.
+ * 
+ * @author Olivia Lang
+ * @see scriptmanager.objects.ArchTEx.CorrParameter
+ * @see scriptmanager.scripts.BAM_Statistics.CrossCorrelation
+ */
+@Command(name = "cross-corr", mixinStandardHelpOptions = true,
+	description = ToolDescriptions.archtex_crosscorrelation_description,
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
+	sortOptions = false,
+	exitCodeOnInvalidInput = 1,
+	exitCodeOnExecutionException = 1)
+public class CrossCorrelationCLI implements Callable<Integer> {
+
+	@Parameters( index = "0", description = "The BAM file to perform the cross-correlation on")
+	private File bamFile;
+
+	@Option(names = {"-o", "--output"}, description = "specify output basename, default is the BAM input filename without extension")
+	private File outputBasename = null;
+
+	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect correlation strategy:%n\t@|fg(red) (select no more than one of these options)|@%n")
+	CorrType corrType = new CorrType();
+	static class CorrType {
+		@Option(names = {"-g", "--genome"}, description = "Use the full genome correlation method")
+		private boolean corrGenome = false;
+		@Option(names = {"-r", "--random"}, description = "Use the random sampling correlation method (default)")
+		private boolean corrRandom = false;
+	}
+
+	@Option(names = {"-t", "--cpu"}, description = "set number of threads for performance tuning (default=1)")
+	private int cpu = 1;
+
+	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nRandom Sampling Options:%n\t@|fg(red) (ignored if full genome correlation method selected)|@%n")
+	SamplingParams samplingParams = new SamplingParams();
+	static class SamplingParams {
+		@Option(names = {"-w", "--window"}, description = "set window frame size for each extraction (default=50kb)")
+		private int windowSize = 50000;
+		@Option(names = {"-i", "--iterations"}, description = "set number of random iterations per chromosome (default=10)")
+		private int iterations = 10;
+	}
+
+	CorrParameter param = new CorrParameter();
+
+	@Override
+	public Integer call() throws Exception {
+		System.err.println( ">CrossCorrelationCLI.call()" );
+		String validate = validateInput();
+		if(!validate.equals("")){
+			System.err.println( validate );
+			System.err.println("Invalid input. Check usage using '-h' or '--help'");
+			System.exit(1);
+		}
+
+		CrossCorrelation.correlate( outputBasename, bamFile, param, null);
+
+		System.err.println("Calculations Complete");
+		return(0);
+	}
+
+	/**
+	 * Validate the input values before executing the script.
+	 * 
+	 * @return a multi-line string describing input validation issues
+	 * @throws IOException
+	 */
+	private String validateInput() throws IOException {
+		String r = "";
+
+		//check inputs exist
+		if(!bamFile.exists()){
+			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
+			return(r);
+		}
+		//check BAI exists
+		File f = new File(bamFile+".bai");
+		if(!f.exists() || f.isDirectory()){
+			r += "(!)BAI Index File does not exist for: " + bamFile.getName() + "\n";
+		}
+		//set default output filename
+		if(outputBasename==null){
+// 			output = new File("output_bam_stats.txt");		//this default name mimics the gui
+			outputBasename = new File(ExtensionFileFilter.stripExtension(bamFile) + "_CrossCorrelation.txt");
+		//check output filename is valid
+		}else{
+			//no check ext
+			//check directory
+			if(outputBasename.getParent()==null){
+// 				System.err.println("default to current directory");
+			} else if(!new File(outputBasename.getParent()).exists()){
+				r += "(!)Check output directory exists: " + outputBasename.getParent() + "\n";
+			}
+		}
+
+		//validate random sampling params
+		if (corrType.corrGenome) {
+			param.setCorrType(true);
+		} else {
+			param.setCorrType(false);
+			if (samplingParams.windowSize<1) { r += "(!)Window size must be at least 1\n"; }
+			if (samplingParams.iterations<1) { r += "(!)Num iterations must be at least 1\n"; }
+			param.setWindow(samplingParams.windowSize);
+		}
+		// valiate CPU
+		if (cpu<1) { r += "(!)CPU count must be at least 1\n"; }
+		param.setThreads(cpu);
+
+		return(r);
+	}
+}

src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFCLI.java

@@ -82,4 +82,12 @@ private String validateInput() throws IOException {
 
 		return(r);
 	}
+
+	public static String getCLIcommand(File OUTPUT, File BED, boolean gzOutput) {
+		String command = "java -jar $SCRIPTMANAGER coordinate-manipulation bed-to-gff";
+		command += " " + BED.getAbsolutePath();
+		command += gzOutput ? " -z" : "";
+		command += " -o " + OUTPUT;
+		return(command);
+	}
 }

src/main/java/scriptmanager/cli/Read_Analysis/TagPileupCLI.java

@@ -110,6 +110,8 @@ static class CalcOptions{
 		private int shift = 0;
 		@Option(names = {"-b", "--bin-size"}, description = "set a bin size for the output (default=1bp)")
 		private int binSize = 1;
+		@Option(names = {"-e", "--tag-extend"}, description = "set a bp length to extend the tag (default=0)")
+		private int tagExtend = 0;
 		@Option(names = {"-t", "--standard"}, description = "set tags to be equal (default=false)")
 		private boolean tagsEqual;
 		@Option(names = {"--cpu"}, description = "set number of CPUs to use (default=1)")
@@ -275,6 +277,7 @@ private String validateInput() throws IOException {
 		//Set SHIFT, BIN, CPU
 		p.setShift(calcOptions.shift);
 		p.setBin(calcOptions.binSize);
+		p.setTagExtend(calcOptions.tagExtend);
 		p.setCPU(calcOptions.cpu);
 
 		//Set BLACKLIST & STANDARD
@@ -298,4 +301,13 @@ private String validateInput() throws IOException {
 		return(r);
 	}
 
+	public static String getCLIcommand(File BED, File BAM, PileupParameters PARAM) {
+		String command = "java -jar $SCRIPTMANAGER read-analysis tag-pileup";
+		command += " " + PARAM.getCLIOptions();
+		command += " " + BED.getAbsolutePath();
+		command += " " + BAM.getAbsolutePath();
+		String NAME = PARAM.getOutputDirectory() + File.separator + PARAM.generateFileBase(BED.getName(), BAM.getName());
+		command += " -M " + NAME + " -o " + NAME;
+		return(command);
+	}
 }