Wrapped priority Picard tools (#122) and added program record to Filter PIP-seq output (#144)

.classpath

@@ -6,20 +6,6 @@
 			<attribute name="gradle_used_by_scope" value="main,test"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="bin/test" path="src/test/java">
-		<attributes>
-			<attribute name="gradle_scope" value="test"/>
-			<attribute name="gradle_used_by_scope" value="test"/>
-			<attribute name="test" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="bin/test" path="src/test/resources">
-		<attributes>
-			<attribute name="gradle_scope" value="test"/>
-			<attribute name="gradle_used_by_scope" value="test"/>
-			<attribute name="test" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="src" output="bin/main" path="src/main/java">
 		<attributes>
 			<attribute name="gradle_scope" value="main"/>
@@ -29,4 +15,4 @@
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8/"/>
 	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
 	<classpathentry kind="output" path="bin/default"/>
-</classpath>
+</classpath>

.project

@@ -20,4 +20,15 @@
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
 	</natures>
+	<filteredResources>
+		<filter>
+			<id>1731979070369</id>
+			<name></name>
+			<type>30</type>
+			<matcher>
+				<id>org.eclipse.core.resources.regexFilterMatcher</id>
+				<arguments>node_modules|\.git|__CREATED_BY_JAVA_LANGUAGE_SERVER__</arguments>
+			</matcher>
+		</filter>
+	</filteredResources>
 </projectDescription>

.settings/org.eclipse.buildship.core.prefs

@@ -1,2 +1,13 @@
+arguments=--init-script /var/folders/vs/qy0cxq3x47v2gjsbgwxmt14r0000gn/T/db3b08fc4a9ef609cb16b96b200fa13e563f396e9bb1ed0905fdab7bc3bc513b.gradle --init-script /var/folders/vs/qy0cxq3x47v2gjsbgwxmt14r0000gn/T/52cde0cfcf3e28b8b7510e992210d9614505e0911af0c190bd590d7158574963.gradle
+auto.sync=false
+build.scans.enabled=false
+connection.gradle.distribution=GRADLE_DISTRIBUTION(WRAPPER)
 connection.project.dir=
-eclipse.preferences.version=1
+eclipse.preferences.version=1
+gradle.user.home=
+java.home=/Library/Java/JavaVirtualMachines/jdk-22.jdk/Contents/Home
+jvm.arguments=
+offline.mode=false
+override.workspace.settings=true
+show.console.view=true
+show.executions.view=true

src/main/java/scriptmanager/main/ScriptManagerGUI.java

@@ -115,6 +115,10 @@ public void run() {
 		// CrossCorrelation
 		pnlStat.add(initializeToolPanel("Cross Correlation", ToolDescriptions.archtex_crosscorrelation_description,
 				Class.forName("scriptmanager.window_interface.BAM_Statistics.CrossCorrelationWindow")));
+
+		// CollectBaseDistributionByCycle
+		pnlStat.add(initializeToolPanel("Collect BAM Distribution", ToolDescriptions.collect_base_distribution_by_cycle_description,
+				Class.forName("scriptmanager.window_interface.BAM_Statistics.CollectBaseDistributionByCycleWindow")));
 
 		// ======== BAM_Manipulation ========
 		JPanel pnlBamManip = new JPanel();
@@ -138,6 +142,26 @@ public void run() {
 		// FilterPIPseq
 		pnlBamManip.add(initializeToolPanel("Filter for PIP-seq", ToolDescriptions.filter_pip_seq_description,
 				Class.forName("scriptmanager.window_interface.BAM_Manipulation.FilterforPIPseqWindow")));
+
+		// DownsampleSAM
+		pnlBamManip.add(initializeToolPanel("Downsample SAM/BAM", ToolDescriptions.downsample_sam_description,
+				Class.forName("scriptmanager.window_interface.BAM_Manipulation.DownsampleSamWindow")));
+
+		// ValidateSAMFile
+		pnlBamManip.add(initializeToolPanel("Validate SAM/BAM", ToolDescriptions.validate_sam_file_description,
+		Class.forName("scriptmanager.window_interface.BAM_Manipulation.ValidateSamWindow")));
+
+		// NormalizeFasta
+		pnlBamManip.add(initializeToolPanel("Normalize FASTA File", ToolDescriptions.normalize_fasta_description,
+		Class.forName("scriptmanager.window_interface.BAM_Manipulation.NormalizeFastaWindow")));
+
+		// FilterSAMReads
+		pnlBamManip.add(initializeToolPanel("Filter BAM Reads", ToolDescriptions.filter_sam_reads_description,
+		Class.forName("scriptmanager.window_interface.BAM_Manipulation.FilterSamReadsWindow")));
+
+		// FilterSAMReads
+		pnlBamManip.add(initializeToolPanel("Add Comments to BAM", ToolDescriptions.add_comments_to_bam_description,
+		Class.forName("scriptmanager.window_interface.BAM_Manipulation.AddCommentsToBamWindow")));
 
 		// ======== BAM_Format_Converter ========
 		JPanel pnlBamConvert = new JPanel();
@@ -160,6 +184,14 @@ public void run() {
 		pnlBamConvert.add(initializeToolPanel("BAM to bedGraph", ToolDescriptions.bam_to_bedgraph_description,
 				Class.forName("scriptmanager.window_interface.BAM_Format_Converter.BAMtobedGraphWindow")));
 
+		// SAMtoFASTQ
+		pnlBamConvert.add(initializeToolPanel("BAM to FASTQ", ToolDescriptions.sam_to_fastq_description,
+		Class.forName("scriptmanager.window_interface.BAM_Format_Converter.SamtoFastqWindow")));
+
+		// SAMFormatConverter
+		pnlBamConvert.add(initializeToolPanel("SAM to BAM or BAM to SAM", ToolDescriptions.sam_to_fastq_description,
+		Class.forName("scriptmanager.window_interface.BAM_Format_Converter.SamFormatConverterWindow")));
+
 		// ======== File_Utilities ========
 		JPanel pnlFileUtility = new JPanel();
 		BoxLayout bl_pnlFileUtility = new BoxLayout(pnlFileUtility, BoxLayout.PAGE_AXIS);

src/main/java/scriptmanager/objects/ToolDescriptions.java

@@ -33,6 +33,7 @@ public class ToolDescriptions {
 	public static final String se_stat_description = "Output BAM Header including alignment statistics and parameters given any indexed (BAI) BAM File.";
 	public static final String pe_stat_description = "Generates Insert-size Histogram statistics (GEO requirement) and outputs BAM Header including alignment statistics and parameters given a sorted and indexed (BAI) paired-end BAM File.";
 	public static final String bam_correlation_description = "Genome-Genome correlations for replicate comparisons given multiple sorted and indexed (BAI) BAM files.";
+	public static final String collect_base_distribution_by_cycle_description = "Chart the nucleotide distribution per cycle in a BAM file";
 	public static final String archtex_crosscorrelation_description = ("Calculate optimal tag shift based on ArchTEx implementation (PMID:22302569)");
 
 	// BAM Manipulation
@@ -41,12 +42,19 @@ public class ToolDescriptions {
 	public static final String remove_duplicates_description = "Removes duplicate reads in Paired-End sequencing given identical 5' read locations. RAM intensive process. If program freezes, increase JAVA heap size."; //*
 	public static final String merge_bam_description = "Merges Multiple BAM files into single BAM file. Sorting is performed automatically. RAM intensive process. If program freezes, increase JAVA heap size."; //*
 	public static final String filter_pip_seq_description = "Filter BAM file by -1 nucleotide. Requires genome FASTA file.";
+	public static final String downsample_sam_description = "Downsample a BAM file to a specified percentage or read count of deterministically random reads.";
+	public static final String validate_sam_file_description = "Validate SAM/BAM files comprehensively, ensuring adherence to the SAM format specification and detecting errors or inconsistencies in alignment data.";
+	public static final String normalize_fasta_description = "Reduce redundant sequences and normalize read coverage in a FASTA file, improving downstream analysis accuracy";
+	public static final String filter_sam_reads_description = "Filter BAM files by applying user-defined filters to include or exclude specific reads based on read lists or genomic intervals";
+	public static final String add_comments_to_bam_description = "Adds comments to the header of a BAM file.";
 
 	// BAM Format Converter
 	public static final String bam_to_scidx_description = "Convert BAM file to scIDX file.";
 	public static final String bam_to_gff_description = "Convert BAM file to GFF file.";
 	public static final String bam_to_bed_description = "Convert BAM file to BED file.";
 	public static final String bam_to_bedgraph_description = "Convert BAM file to bedGraph file.";
+	public static final String sam_to_fastq_description = "Convert BAM file to FASTQ file";
+	public static final String sam_format_converter_description = "Convert SAM file to Bam file or Bam file to Sam file";
 
 	// File Utilities
 	public static final String md5checksum_description = "Calculate MD5 checksum for files.";
@@ -85,7 +93,6 @@ public class ToolDescriptions {
 	public static final String aggregate_data_description = "Compile data from tab-delimited file into matrix according to user-specified metric.";
 	public static final String transpose_matrix_description = "Interchange the rows and columns of tab-delimited matrix data.";
 
-
 	// Sequence Analysis
 	public static final String fasta_extract_description = "Generate FASTA file from indexed Genome FASTA file and BED file. Script will generate FAI index if not present in Genome FASTA folder.";
 	public static final String randomize_fasta_description = "Randomize FASTA sequence for each input entry.";
@@ -101,4 +108,6 @@ public class ToolDescriptions {
 	public static final String composite_description = "Generate a Composite Plot PNG from composite data like the output in TagPileup";
 	public static final String label_heatmap_description = "Create an SVG label for heatmap inputs";
 
+	// Whether or not to log legacy Picard commands
+	public static final boolean picard_legacy_commends = true;
 }

src/main/java/scriptmanager/scripts/BAM_Format_Converter/SamFormatConverterWrapper.java

@@ -0,0 +1,53 @@
+package scriptmanager.scripts.BAM_Format_Converter;
+import htsjdk.samtools.SAMException;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import org.broadinstitute.barclay.argparser.CommandLineParser;
+
+/**
+ * @author Erik Pavloski
+ * @see scriptmanager.window_interface.BAM_Format_Converter.SamFormatConverterWindow
+ * This code runs the Picard tool SamFormatConverter
+ * It can swap a SAM file to a BAM file and vice versa
+ */
+
+public class SamFormatConverterWrapper {
+    /**
+     * @param input the BAM/SAM file to be converted
+     * @param output the output BAM/SAM file
+     *
+     * @throws IOException
+     * @throws SAMException
+     */
+    public static void run(File input, File output) throws IOException, SAMException {
+        System.out.println("Converting file...");
+        // Converts the SAM/BAM file to fastq
+        final picard.sam.SamFormatConverter samFormatConverter = new picard.sam.SamFormatConverter();
+        final ArrayList<String> args = new ArrayList<>();
+        args.add("INPUT=" + input.getAbsolutePath());
+        args.add("OUTPUT=" + output.getAbsolutePath());
+        samFormatConverter.instanceMain(args.toArray(new String[args.size()]));
+        System.out.println("File converted");
+    }
+
+    /**
+	 * Reconstruct CLI command
+     * 
+     * @param input the BAM/SAM file to be converted
+     * @param output the output BAM/SAM file
+     */
+    public static String getCLIcommand(File input, File output) {
+        String command = "java -jar $PICARD ";
+        final CommandLineParser parser = new picard.sam.SamFormatConverter().getCommandLineParser();
+        final ArrayList<String> args = new ArrayList<>();
+        args.add("INPUT=" + input.getAbsolutePath());
+        args.add("OUTPUT=" + output.getAbsolutePath());
+        String[] argv = args.toArray(new String[args.size()]);
+        parser.parseArguments(System.err, argv);
+        command += parser.getCommandLine();
+        return command;
+    }
+}

src/main/java/scriptmanager/scripts/BAM_Format_Converter/SamtoFastqWrapper.java

@@ -0,0 +1,77 @@
+package scriptmanager.scripts.BAM_Format_Converter;
+import htsjdk.samtools.SAMException;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import org.broadinstitute.barclay.argparser.CommandLineParser;
+
+/**
+ * @author Erik Pavloski
+ * @see scriptmanager.window_interface.BAM_Format_Converter.SamtoFastqWindow
+ * This code runs the Picard tool SamtoFastq
+ */
+
+public class SamtoFastqWrapper {
+    /**
+     * @param input the BAM/SAM file to be converted
+     * @param output the output fastq file
+     * @param compress a boolean to determine whether to compress the output or not
+     *                 default = false = do not compress
+     * @param perRG a boolean to determine whether to output per read group. Compress does this as well
+     * @param outputDir the output directory
+     * @throws IOException
+     * @throws SAMException
+     */
+    public static void run(File input, File output, boolean compress, boolean perRG, File outputDir) throws IOException, SAMException {
+
+        System.out.println("Converting file...");
+            // Converts the SAM/BAM file to fastq
+            final picard.sam.SamToFastq samToFastq = new picard.sam.SamToFastq();
+            final ArrayList<String> args = new ArrayList<>();
+            args.add("INPUT=" + input.getAbsolutePath());
+            if (compress) {
+                args.add("OUTPUT_DIR=" + outputDir.getCanonicalPath());
+                args.add("COMPRESS_OUTPUTS_PER_RG=" + true);
+            } else if (perRG) {
+                args.add("OUTPUT_DIR=" + outputDir.getCanonicalPath());
+                args.add("OUTPUT_PER_RG=" + true);
+            } else {
+                args.add("FASTQ=" + output.getAbsolutePath());
+            }
+            samToFastq.instanceMain(args.toArray(new String[args.size()]));
+        System.out.println("File converted");
+    }
+
+    /**
+	 * Reconstruct CLI command
+     * 
+     * @param input the BAM/SAM file to be converted
+     * @param output the output fastq file
+     * @param compress a boolean to determine whether to compress the output or not
+     *                 default = false = do not compress
+     * @param perRG a boolean to determine whether to output per read group. Compress does this as well
+     * @param outputDir the output directory
+     * @throws IOException
+     */
+    public static String getCLIcommand(File input, File output, boolean compress, boolean perRG, File outputDir) throws IOException {
+        String command = "java -jar $PICARD ";
+        final CommandLineParser parser = new picard.sam.SamToFastq().getCommandLineParser();
+        final ArrayList<String> args = new ArrayList<>();
+        args.add("INPUT=" + input.getAbsolutePath());
+        if (compress) {
+            args.add("OUTPUT_DIR=" + outputDir.getCanonicalPath());
+            args.add("COMPRESS_OUTPUTS_PER_RG=" + true);
+        } else if (perRG) {
+            args.add("OUTPUT_DIR=" + outputDir.getCanonicalPath());
+            args.add("OUTPUT_PER_RG=" + true);
+        } else {
+            args.add("FASTQ=" + output.getAbsolutePath());
+        }
+        String[] argv = args.toArray(new String[args.size()]);
+        parser.parseArguments(System.err, argv);
+        command += parser.getCommandLine();
+        return command;
+    }
+}

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

@@ -0,0 +1,82 @@
+package scriptmanager.scripts.BAM_Manipulation;
+
+import htsjdk.samtools.BamFileIoUtils;
+import htsjdk.samtools.SAMException;
+import htsjdk.samtools.SAMProgramRecord;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import picard.cmdline.CommandLineSyntaxTranslater;
+import picard.sam.AddCommentsToBam;
+import scriptmanager.objects.ToolDescriptions;
+import scriptmanager.util.BAMUtilities;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.nio.file.Files;
+import java.util.ArrayList;
+
+import org.broadinstitute.barclay.argparser.CommandLineParser;
+
+/**
+ * @author Erik Pavloski
+ * This is the Wrapper class for the AddCommentsToBam Picard tool
+ * @see scriptmanager.window_interface.BAM_Manipulation.AddCommentsToBamWindow
+ */
+public class AddCommentsToBamWrapper {
+    /**
+     * @param input the bam file to add comments to
+     * @param output the output file
+     *
+     * @throws IOException
+     * @throws SAMException
+     */
+    public static void run(File input, File output, ArrayList<String> comments) throws IOException, SAMException {
+        System.out.println("Add Comments To Bam");
+
+        final picard.sam.AddCommentsToBam addComments = new picard.sam.AddCommentsToBam();
+        final ArrayList<String> args = new ArrayList<>();
+        args.add("INPUT=" + input.getAbsolutePath());
+        args.add("OUTPUT=" + output.getAbsolutePath());
+        for (String c: comments){
+            args.add("C=" + c);
+        }
+        addComments.instanceMain(args.toArray(new String[args.size()]));
+
+        // Copy output
+        File temp  = new File(output.toPath() + "copy");
+        Files.copy(output.toPath(), new PrintStream(temp));
+        // Create and add new record
+		SamReader reader = SamReaderFactory.makeDefault().open(temp);
+        String command = AddCommentsToBamWrapper.getCLIcommand(input, output, comments);
+        SAMProgramRecord newRecord = BAMUtilities.getPGRecord(reader.getFileHeader(), addComments.getClass().getSimpleName(),  command, addComments.getVersion());
+        reader.getFileHeader().addProgramRecord(newRecord);
+		BamFileIoUtils.reheaderBamFile(reader.getFileHeader(), temp, output, false, false);
+        // Delete copy
+        temp.delete();
+        System.out.println("SAM/BAM file downsampled");
+
+        System.out.println("Comments Added");
+    }
+
+    /**
+	 * Reconstruct CLI command
+     * 
+     * @param input the bam file to add comments to
+     * @param output the output file
+     */
+    public static String getCLIcommand(File input, File output, ArrayList<String> comments) {
+        String command = "java -jar $PICARD ";
+        final CommandLineParser parser = new picard.sam.AddCommentsToBam().getCommandLineParser();
+        final ArrayList<String> args = new ArrayList<>();
+        args.add("INPUT=" + input.getAbsolutePath());
+        args.add("OUTPUT=" + output.getAbsolutePath());
+        for (String c: comments){
+            args.add("C=" + c);
+        }
+        String[] argv = args.toArray(new String[args.size()]);
+        parser.parseArguments(System.err, argv);
+        command += parser.getCommandLine();
+        return command;
+    }
+}