From 40f853f2eadd8c10bc722e39ea795925e28e001a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= <seb.schoenherr@gmail.com>
Date: Fri, 31 May 2024 12:46:28 +0200
Subject: [PATCH] Fix missing contigs

---
 .../mut/commands/StatisticsCommand.java       | 35 ++++++++-----------
 .../java/genepi/mut/steps/StatisticsTest.java | 19 +++++++++-
 2 files changed, 32 insertions(+), 22 deletions(-)

diff --git a/src/main/java/genepi/mut/commands/StatisticsCommand.java b/src/main/java/genepi/mut/commands/StatisticsCommand.java
index 02ccb37..960f596 100644
--- a/src/main/java/genepi/mut/commands/StatisticsCommand.java
+++ b/src/main/java/genepi/mut/commands/StatisticsCommand.java
@@ -99,7 +99,6 @@ public Integer call() throws IOException {
 			try {
 				reader = new BufferedReader(new FileReader(mapping));
 			} catch (FileNotFoundException e) {
-				// TODO Auto-generated catch block
 				e.printStackTrace();
 				return -1;
 			}
@@ -129,7 +128,7 @@ public Integer call() throws IOException {
 		}
 
 		for (StatisticsFile sample : samples) {
-
+			
 			if (sample.getReadGroup() == null) {
 				{
 					countNoReadGroups++;
@@ -223,26 +222,20 @@ public Integer call() throws IOException {
 		text.append("Input Samples: " + samples.size() + "\n");
 		text.append("Passed Samples: " + validFiles + "\n");
 
-		if (contigs.size() > 1) {
-			context.error("Different contigs have been detected");
-			System.out.println("\n\nERROR: Different contigs have been detected for your input samples. Please upload them in different batches.");
+		
+		if (contigs.size() == 0) {
+			context.error("No valid mtDNA contigs with length 16569 have been detected in your input files.");
+			System.out.println("\n\nERROR: No valid mtDNA contigs detected.");
 			return -1;
-		} else {
-			text.append("Detected contig name: " + contigs.get(0) + "\n");
 		}
-
-		/*
-		 * if (tool.equals("mutect2") || tool.equals("fusion")) {
-		 * 
-		 * boolean found = false; for (String contig : allowed_contigs) { if
-		 * (contig.equals(contigs.get(0))) { found = true; } }
-		 * 
-		 * if (!found) { context.
-		 * error("For Mutect2, please one of the following contig names for chromosome MT: "
-		 * + allowed_contigs.toString()); return -1; }
-		 * 
-		 * }
-		 */
+	
+		if (contigs.size() != 1) {
+			context.error("Different mtDNA contig names have been detected in your input files.");
+			System.out.println("\n\nERROR: Different contig names have been detected for your input samples. Please upload them in different batches.");
+			return -1;
+		}
+		
+		text.append("Detected mtDNA contig name: " + contigs.get(0) + "\n");
 
 		if (lowestMeanDepth != -1) {
 			text.append("Min Mean Depth: " + lowestMeanDepth + "\n");
@@ -306,7 +299,7 @@ public Integer call() throws IOException {
 			System.out.println("\n\nERROR: No input samples passed the QC step.");
 			return -1;
 		} else {
-			context.ok("Input Validation run succesfully, mtDNA analysis can be started.");
+			context.ok("Input Validation finished successfully, mtDNA analysis can be started.");
 			return 0;
 		}
 		
diff --git a/src/test/java/genepi/mut/steps/StatisticsTest.java b/src/test/java/genepi/mut/steps/StatisticsTest.java
index 5bcb204..af8ffaa 100644
--- a/src/test/java/genepi/mut/steps/StatisticsTest.java
+++ b/src/test/java/genepi/mut/steps/StatisticsTest.java
@@ -48,7 +48,7 @@ public void testWithTwoContigs() throws Exception {
 		
 		CloudgeneReport CloudgeneLog = new CloudgeneReport(CLOUDGENE_LOG);
 
-		assertTrue(CloudgeneLog.hasInMemory("Different contigs have been detected"));
+		assertTrue(CloudgeneLog.hasInMemory("Different mtDNA contig names have been detected in your input files."));
 		assertTrue(CloudgeneLog.hasInMemory("[ERROR]"));
 
 
@@ -106,6 +106,23 @@ public void testWithNoContig() throws Exception {
 		assertTrue(CloudgeneLog.hasInMemory("Passed Samples: 1"));
 
 
+	}
+	
+	@Test
+	public void testWithMissingContig() throws Exception {
+
+		String inputFolder = "test-data/statistics/sample_statistics_missing_contig.txt";
+
+
+		StatisticsCommand command = new StatisticsCommand();
+		command.setInput(inputFolder);
+		command.setOutput("excluded_samples.txt");
+
+		assertEquals(-1, (int) command.call());
+		
+
+
+
 	}