Update chunks writer

genepi · Jul 29, 2024 · 3b73ee2 · 3b73ee2
1 parent 4b0d191
commit 3b73ee2
Showing 1 changed file with 9 additions and 6 deletions.
diff --git a/src/main/java/genepi/imputationserver/steps/fastqc/io/ExcludedChunksWriter.java b/src/main/java/genepi/imputationserver/steps/fastqc/io/ExcludedChunksWriter.java
@@ -2,13 +2,14 @@
 
 import genepi.imputationserver.steps.vcf.MinimalVariantContext;
 import genepi.imputationserver.steps.vcf.VcfChunk;
+import genepi.io.table.writer.CsvTableWriter;
 import genepi.io.text.LineWriter;
 
 import java.io.IOException;
 
 public class ExcludedChunksWriter {
 
-    private LineWriter writer;
+    private CsvTableWriter writer;
 
     private String filename;
 
@@ -18,12 +19,14 @@ public ExcludedChunksWriter(String filename) throws IOException {
 
     public void write(VcfChunk chunk, double overlap, int countLowSamples) throws IOException {
         if (writer == null) {
-            writer = new LineWriter(filename);
-            writer.write(
-                    "#Chunk" + "\t" + "SNPs (#)" + "\t" + "Reference Overlap (%)" + "\t" + "Low Sample Call Rates (#)",
-                    false);
+            writer = new CsvTableWriter(filename, '\t', false);
+            writer.setColumns(new String[]{"CHUNK", "SNPS", "REFERENCE_OVERLAP", "SAMPLES_LOW_CALL_RATE"});
         }
-        writer.write(chunk.toString() + "\t" + chunk.overallSnpsChunk + "\t" + overlap + "\t" + countLowSamples);
+        writer.setString("CHUNK", chunk.toString());
+        writer.setInteger("SNPS", chunk.overallSnpsChunk);
+        writer.setDouble("REFERENCE_OVERLAP", overlap);
+        writer.setInteger("SAMPLES_LOW_CALL_RATE", countLowSamples);
+        writer.next();
     }
 
     public void close() throws IOException {