Merge branch 'features/msav-support' of https://github.com/genepi/imp…

…utationserver into releases/1.8.0-beta3

files/imputationserver-beagle.yaml

@@ -1,7 +1,7 @@
 id: imputationserver-beagle
 name: Genotype Imputation supporting Beagle (Minimac4)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.7.4
+version: 1.8.0-beta3
 website: https://imputationserver.readthedocs.io
 category:
 

files/imputationserver-hla.yaml

@@ -1,7 +1,7 @@
 id: imputationserver-hla
 name: Genotype Imputation HLA (Minimac4)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.7.4
+version: 1.8.0-beta3
 website: https://imputationserver.readthedocs.io
 category:
 

files/imputationserver-pgs.yaml

@@ -1,7 +1,7 @@
 id: imputationserver-pgs
 name: Genotype Imputation (PGS Calc Integration)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.7.4
+version: 1.8.0-beta3
 website: https://imputationserver.readthedocs.io
 category:
 

files/minimac4.yaml

@@ -1,7 +1,7 @@
 id: imputationserver
 name: Genotype Imputation (Minimac4)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.7.4
+version: 1.8.0-beta3
 website: https://imputationserver.readthedocs.io
 category:
 

pom.xml

@@ -5,11 +5,8 @@
 
 	<groupId>genepi</groupId>
 	<artifactId>imputationserver</artifactId>
-
-	<version>1.7.4</version>
-
+	<version>1.8.0-beta3</version>
 	<packaging>jar</packaging>
-
 	<name>University of Michigan Imputation Server</name>
 	<url>http://maven.apache.org</url>
 

src/main/java/genepi/imputationserver/steps/imputation/ImputationMapper.java

@@ -117,7 +117,6 @@ protected void setup(Context context) throws IOException, InterruptedException {
 		String referenceName = parameters.get(ImputationJob.REF_PANEL);
 		imputationParameters.setPhasing(phasingEngine);
 		imputationParameters.setReferencePanelName(referenceName);
-		imputationParameters.setMinR2(minR2);
 		imputationParameters.setPhasingRequired(phasingRequired);
 
 		// get cached files
@@ -153,11 +152,11 @@ protected void setup(Context context) throws IOException, InterruptedException {
 			mapBeagleFilename = cache.getFile(mapBeagle);
 		}
 
-		String minimacCommand = cache.getFile("Minimac4");
+		String minimacCommand = cache.getFile("minimac4");
 		String eagleCommand = cache.getFile("eagle");
 		String beagleCommand = cache.getFile("beagle.jar");
 		String tabixCommand = cache.getFile("tabix");
-		
+
 		// create temp directory
 		DefaultPreferenceStore store = new DefaultPreferenceStore(context.getConfiguration());
 		folder = store.getString("minimac.tmp");
@@ -182,9 +181,9 @@ protected void setup(Context context) throws IOException, InterruptedException {
 				String formatFile = cache.getFile(name + ".format");
 				if (formatFile != null) {
 					// create symbolic link to format file. they have to be in the same folder
-					Files.createSymbolicLink(Paths.get(FileUtil.path(folder,name)), Paths.get(localFilename));
-					Files.createSymbolicLink(Paths.get(FileUtil.path(folder,name+".format")), Paths.get(formatFile));
-					scores[i] = FileUtil.path(folder,name);
+					Files.createSymbolicLink(Paths.get(FileUtil.path(folder, name)), Paths.get(localFilename));
+					Files.createSymbolicLink(Paths.get(FileUtil.path(folder, name + ".format")), Paths.get(formatFile));
+					scores[i] = FileUtil.path(folder, name);
 				}
 			}
 			System.out.println("Loaded " + scores.length + " score files from distributed cache");
@@ -212,6 +211,7 @@ protected void setup(Context context) throws IOException, InterruptedException {
 		int phasingWindow = Integer.parseInt(store.getString("phasing.window"));
 
 		int window = Integer.parseInt(store.getString("minimac.window"));
+		int decay = Integer.parseInt(store.getString("minimac.decay"));
 
 		String minimacParams = store.getString("minimac.command");
 		String eagleParams = store.getString("eagle.command");
@@ -226,6 +226,8 @@ protected void setup(Context context) throws IOException, InterruptedException {
 		pipeline.setPhasingWindow(phasingWindow);
 		pipeline.setBuild(build);
 		pipeline.setMinimacWindow(window);
+		pipeline.setMinR2(minR2);
+		pipeline.setDecay(decay);
 
 	}
 
@@ -289,16 +291,8 @@ public void map(LongWritable key, Text value, Context context) throws IOExceptio
 				statistics.setImportTime((end - start) / 1000);
 
 			} else {
-				if (imputationParameters.getMinR2() > 0) {
-					// filter by r2
-					String filteredInfoFilename = outputChunk.getInfoFilename() + "_filtered";
-					filterInfoFileByR2(outputChunk.getInfoFilename(), filteredInfoFilename,
-							imputationParameters.getMinR2());
-					HdfsUtil.put(filteredInfoFilename, HdfsUtil.path(output, chunk + ".info"));
-
-				} else {
-					HdfsUtil.put(outputChunk.getInfoFilename(), HdfsUtil.path(output, chunk + ".info"));
-				}
+
+				HdfsUtil.put(outputChunk.getInfoFilename(), HdfsUtil.path(output, chunk + ".info"));
 
 				long start = System.currentTimeMillis();
 

src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java

@@ -24,9 +24,9 @@
 
 public class ImputationPipeline {
 
-	public static final String PIPELINE_VERSION = "michigan-imputationserver-1.7.4";
+	public static final String PIPELINE_VERSION = "michigan-imputationserver-1.8.0-beta3";
 
-	public static final String IMPUTATION_VERSION = "minimac4-1.0.2";
+	public static final String IMPUTATION_VERSION = "minimac-v4.1.5";
 
 	public static final String BEAGLE_VERSION = "beagle.18May20.d20.jar";
 
@@ -48,8 +48,12 @@ public class ImputationPipeline {
 
 	private int minimacWindow;
 
+	private int minimacDecay;
+
 	private int phasingWindow;
 
+	private double minR2;
+
 	private String refFilename;
 
 	private String mapMinimac;
@@ -288,6 +292,16 @@ public boolean phaseWithBeagle(VcfChunk input, VcfChunkOutput output, String ref
 	public boolean imputeVCF(VcfChunkOutput output)
 			throws InterruptedException, IOException, CompilationFailedException {
 
+		// create tabix index
+		Command tabix = new Command(tabixCommand);
+		tabix.setSilent(false);
+		tabix.setParams(output.getPhasedVcfFilename());
+		System.out.println("Command: " + tabix.getExecutedCommand());
+		if (tabix.execute() != 0) {
+			System.out.println("Error during index creation: " + tabix.getStdOut());
+			return false;
+		}
+
 		String chr = "";
 		if (build.equals("hg38")) {
 			chr = "chr" + output.getChromosome();
@@ -306,6 +320,8 @@ public boolean imputeVCF(VcfChunkOutput output)
 		binding.put("chr", chr);
 		binding.put("unphased", false);
 		binding.put("mapMinimac", mapMinimac);
+		binding.put("minR2", minR2);
+		binding.put("decay", minimacDecay);
 
 		String[] params = createParams(minimacParams, binding);
 
@@ -345,11 +361,11 @@ private boolean runPgsCalc(VcfChunkOutput output) {
 			task.setVcfFilename(output.getImputedVcfFilename());
 			task.setChunk(scoreChunk);
 			task.setRiskScoreFilenames(scores);
-			
-			//TODO: enable fix-strand-flips
-			//task.setFixStrandFlips(true);
-			//task.setRemoveAmbiguous(true);
-			
+
+			// TODO: enable fix-strand-flips
+			// task.setFixStrandFlips(true);
+			// task.setRemoveAmbiguous(true);
+
 			for (String file : scores) {
 				String autoFormat = file + ".format";
 				if (new File(autoFormat).exists()) {
@@ -474,4 +490,13 @@ public void setMapBeagleFilename(String mapBeagleFilename) {
 		this.mapBeagleFilename = mapBeagleFilename;
 	}
 
+	public void setMinR2(double minR2) {
+		this.minR2 = minR2;
+	}
+
+	public void setDecay(int decay) {
+		this.minimacDecay = decay;
+
+	}
+
 }

src/main/java/genepi/imputationserver/util/DefaultPreferenceStore.java

@@ -71,11 +71,12 @@ public static Properties defaults() {
 		defaults.setProperty("chunksize", "20000000");
 		defaults.setProperty("phasing.window", "5000000");
 		defaults.setProperty("minimac.window", "500000");
+		defaults.setProperty("minimac.decay", "0");
 		defaults.setProperty("minimac.sendmail", "no");
 		defaults.setProperty("server.url", "https://imputationserver.sph.umich.edu");
 		defaults.setProperty("minimac.tmp", "/tmp");
 		defaults.setProperty("minimac.command",
-				"--refHaps ${ref} --haps ${vcf} --start ${start} --end ${end} --window ${window} --prefix ${prefix} --chr ${chr} --cpus 1 --noPhoneHome --format GT,DS,GP --allTypedSites --meta --minRatio 0.00001 ${chr =='MT' ? '--myChromosome ' + chr : ''} ${unphased ? '--unphasedOutput' : ''} ${mapMinimac != null ? '--referenceEstimates --map ' + mapMinimac : ''}");
+				"--region ${chr}:${start}-${end} --overlap ${window} --output ${prefix}.dose.vcf.gz --output-format vcf.gz --format GT,DS,GP,HDS --min-ratio 0.00001 --decay ${decay} --all-typed-sites --sites ${prefix}.info --empirical-output ${prefix}.empiricalDose.vcf.gz ${minR2 != 0 ? '--min-r2 ' + minR2 : ''}  ${mapMinimac != null ? '--map ' + mapMinimac : ''} ${ref} ${vcf}");
 		defaults.setProperty("eagle.command",
 				"--vcfRef ${ref} --vcfTarget ${vcf} --geneticMapFile ${map} --outPrefix ${prefix} --bpStart ${start} --bpEnd ${end} --allowRefAltSwap --vcfOutFormat z --keepMissingPloidyX");
 		defaults.setProperty("beagle.command",

src/main/java/genepi/imputationserver/util/FileMerger.java

@@ -24,35 +24,18 @@ public static void splitIntoHeaderAndData(String input, OutputStream outHeader,
 
 		while (reader.next()) {
 			String line = reader.get();
+
 			if (!line.startsWith("#")) {
-				if (parameters.getMinR2() > 0) {
-					// rsq set. parse line and check rsq
-					String info = parseInfo(line);
-					if (info != null) {
-						boolean keep = keepVcfLineByInfo(info, R2_FLAG, parameters.getMinR2());
-						if (keep) {
-							outData.write(line.getBytes());
-							outData.write("\n".getBytes());
-						}
-					} else {
-						// no valid vcf line. keep line
-						outData.write(line.getBytes());
-						outData.write("\n".getBytes());
-					}
-				} else {
-					// no rsq set. keep all lines without parsing
-					outData.write(line.getBytes());
-					outData.write("\n".getBytes());
-				}
+				outData.write(line.getBytes());
+				outData.write("\n".getBytes());
 			} else {
 
 				// write filter command before ID List starting with #CHROM
 				if (line.startsWith("#CHROM")) {
-					outHeader.write(("##pipeline=" + ImputationPipeline.PIPELINE_VERSION + "\n").getBytes());
-					outHeader.write(("##imputation=" + ImputationPipeline.IMPUTATION_VERSION + "\n").getBytes());
-					outHeader.write(("##phasing=" + parameters.getPhasingMethod() + "\n").getBytes());
-					outHeader.write(("##panel=" + parameters.getReferencePanelName() + "\n").getBytes());
-					outHeader.write(("##r2Filter=" + parameters.getMinR2() + "\n").getBytes());
+					outHeader.write(("##mis_pipeline=" + ImputationPipeline.PIPELINE_VERSION + "\n").getBytes());
+					outHeader.write(("##mis_imputation=" + ImputationPipeline.IMPUTATION_VERSION + "\n").getBytes());
+					outHeader.write(("##mis_phasing=" + parameters.getPhasingMethod() + "\n").getBytes());
+					outHeader.write(("##mis_panel=" + parameters.getReferencePanelName() + "\n").getBytes());
 				}
 
 				// write all headers except minimac4 command
@@ -85,9 +68,9 @@ public static void splitPhasedIntoHeaderAndData(String input, OutputStream outHe
 
 				// write filter command before ID List starting with #CHROM
 				if (line.startsWith("#CHROM")) {
-					outHeader.write(("##pipeline=" + ImputationPipeline.PIPELINE_VERSION + "\n").getBytes());
-					outHeader.write(("##phasing=" + parameters.getPhasingMethod() + "\n").getBytes());
-					outHeader.write(("##panel=" + parameters.getReferencePanelName() + "\n").getBytes());
+					outHeader.write(("##mis_pipeline=" + ImputationPipeline.PIPELINE_VERSION + "\n").getBytes());
+					outHeader.write(("##mis_phasing=" + parameters.getPhasingMethod() + "\n").getBytes());
+					outHeader.write(("##mis_panel=" + parameters.getReferencePanelName() + "\n").getBytes());
 				}
 
 				// write all headers except eagle command
@@ -129,24 +112,30 @@ public static void mergeAndGzInfo(List<String> hdfs, String local) throws IOExce
 
 			LineReader reader = new LineReader(in);
 
-			boolean header = true;
+			boolean lineBreak = false;
 
 			while (reader.next()) {
 
 				String line = reader.get();
 
-				if (header) {
+				if (line.startsWith("#")) {
+
 					if (firstFile) {
+
+						if (lineBreak) {
+							out.write('\n');
+						}
 						out.write(line.toString().getBytes());
-						firstFile = false;
+						lineBreak = true;
 					}
-					header = false;
 				} else {
 					out.write('\n');
 					out.write(line.toString().getBytes());
 				}
 			}
 
+			firstFile = false;
+
 			in.close();
 
 		}

src/main/java/genepi/imputationserver/util/ImputationParameters.java

@@ -6,8 +6,6 @@ public class ImputationParameters {
 
 	private String referencePanelName;
 
-	private double minR2;
-
 	private String phasing;
 
 	private boolean phasingRequired;
@@ -20,14 +18,6 @@ public void setReferencePanelName(String referencePanelName) {
 		this.referencePanelName = referencePanelName;
 	}
 
-	public double getMinR2() {
-		return minR2;
-	}
-
-	public void setMinR2(double minR2) {
-		this.minR2 = minR2;
-	}
-
 	public String getPhasing() {
 		return phasing;
 	}