Cell groups

GeneticsHarm · Nov 11, 2016 · 35094f7 · 35094f7
1 parent 35573ab
commit 35094f7
Show file tree

Hide file tree

Showing 4 changed files with 42 additions and 15 deletions.
diff --git a/build.gradle b/build.gradle
@@ -1,5 +1,5 @@
 group 'com.harmbrugge.bamtools'
-version '1.0-SNAPSHOT'
+version '1.0'
 
 apply plugin: 'java'
 

diff --git a/src/main/java/com.harmbrugge.bamtools/BamFileSplitter.java b/src/main/java/com.harmbrugge.bamtools/BamFileSplitter.java
@@ -13,8 +13,7 @@
 import java.io.FileReader;
 import java.io.IOException;
 import java.nio.file.Path;
-import java.util.HashMap;
-import java.util.Map;
+import java.util.*;
 
 /**
  * BamFileSplitter splits a BAM files generated in cell-ranger pipeline from 10xGenomics into a file per singe cell.
@@ -28,12 +27,14 @@ public class BamFileSplitter {
 
     private static final String FILE_NAME_PREFIX = "cell_";
     private static final String EXTENSION = ".bam";
+    private static final int GROUP_SIZE = 50;
 
     private final Log logger = LogFactory.getLog(this.getClass());
     private final Path pathToBarcodeFile;
     private final String outputDir;
 
     private int fileCount;
+    private int groupCount;
     private int recordCount;
     private int absentBarcodeCount;
     private int invalidBarcodeCount;
@@ -52,7 +53,7 @@ public BamFileSplitter(Path pathToBamFile, Path pathToBarcodeFile, Path outputPa
         if (outputPath == null) outputDir = pathToBamFile.getParent() + "/output/";
         else outputDir = outputPath.toString();
 
-        File file = new File(outputDir);
+        File file = new File(outputDir + "/0/");
         if (!file.exists()) file.mkdirs();
 
         this.pathToBarcodeFile = pathToBarcodeFile;
@@ -136,24 +137,39 @@ private boolean isMultimapped(SAMRecord samRecord) {
     private void addRecordToBam(String barcode, SAMRecord samRecord) {
         SAMFileWriter outputBam = outputBams.get(barcode);
 
+        List<SAMReadGroupRecord> readGroup = outputBam.getFileHeader().getReadGroups();
+        if (readGroup.size() > 0) {
+            String readGroupId = readGroup.get(0).getId();
+            samRecord.setAttribute("RG", readGroupId);
+        }
+
         outputBam.addAlignment(samRecord);
     }
 
     private File createBamFile(String barcode) {
         fileCount++;
 
-        String filePath = outputDir + "/" + FILE_NAME_PREFIX + fileCount + "_" + barcode + EXTENSION;
+        if (fileCount % GROUP_SIZE == 0) {
+            groupCount++;
+            File file = new File(outputDir + "/" + groupCount);
+            if (!file.exists()) file.mkdirs();
+        }
+
+        String filePath = outputDir + "/" + groupCount  + "/" + FILE_NAME_PREFIX + fileCount + "_" + barcode + EXTENSION;
         return new File(filePath);
     }
 
     private SAMFileHeader createBamHeader(String barcode) {
         SAMFileHeader samHeader = samReader.getFileHeader();
 
-        SAMReadGroupRecord readGroup = new SAMReadGroupRecord(barcode);
-        readGroup.setSample("cell_" + fileCount);
-        readGroup.setPlatform("Chromium");
+        SAMReadGroupRecord readGroup = new SAMReadGroupRecord(String.valueOf(fileCount));
+        readGroup.setSample("cell_" + fileCount + "_" + barcode);
+        readGroup.setPlatform("ILLUMINA");
+
+        List<SAMReadGroupRecord> readGroups = new ArrayList<>();
+        readGroups.add(readGroup);
 
-        samHeader.addReadGroup(readGroup);
+        samHeader.setReadGroups(readGroups);
 
         return samHeader;
     }

diff --git a/src/main/java/com.harmbrugge.bamtools/Main.java b/src/main/java/com.harmbrugge.bamtools/Main.java
@@ -62,7 +62,7 @@ private void start(String[] args) {
 
                 if (outputPath == null) outputPath = Paths.get(System.getProperty("user.dir"));
 
-                sampleSheetCreator.createSamplesheet(outputPath);
+                sampleSheetCreator.create(outputPath);
             }
         }
         catch (ParseException exp) {

diff --git a/src/main/java/com.harmbrugge.bamtools/SampleSheetCreator.java b/src/main/java/com.harmbrugge.bamtools/SampleSheetCreator.java
@@ -19,15 +19,18 @@ public class SampleSheetCreator {
 
     private static final String SAMPLE_SHEET_FILENAME = "samplesheet.csv";
 
+    private static final int GROUP_SIZE = 50;
+
     private int fileCount;
+    private int groupCount;
 
     private final Path pathToBarcodeFile;
 
     public SampleSheetCreator(Path pathToBarcodeFile) {
          this.pathToBarcodeFile = pathToBarcodeFile;
     }
 
-    public void createSamplesheet(Path outputDir) throws IOException {
+    public void create(Path outputDir) throws IOException {
 
         outputDir.toFile().mkdirs();
         File outputFile = new File(outputDir.toString(), SAMPLE_SHEET_FILENAME);
@@ -36,16 +39,24 @@ public void createSamplesheet(Path outputDir) throws IOException {
         // project,cellId,bamFile
         FileWriter fileWriter = new FileWriter(outputFile.getAbsoluteFile());
         BufferedWriter bw = new BufferedWriter(fileWriter);
-        bw.write("project,cellId,bamFile\n");
+        bw.write("project,cellId,bamFile,cellGroup\n");
 
         try (BufferedReader br = new BufferedReader(new FileReader(pathToBarcodeFile.toFile()))) {
             String barcode = br.readLine();
 
             while (barcode != null) {
                 fileCount++;
-                String filePath = "${splitBamDir}/" + FILENAME_PREFIX + fileCount + "_" + barcode + EXTENSION;
-                bw.write(PROJECT_NAME + "," + FILENAME_PREFIX + fileCount + "_" + barcode + "," + filePath);
-                bw.write("\n");
+
+                if (fileCount % GROUP_SIZE == 0) {
+                    groupCount++;
+                }
+
+                String cellId = FILENAME_PREFIX + fileCount + "_" + barcode;
+                String filePath = groupCount + "/" + cellId + EXTENSION;
+                bw.write(PROJECT_NAME + ",");
+                bw.write(cellId + ",");
+                bw.write(filePath + ",");
+                bw.write(groupCount + "\n");
 
                 barcode = br.readLine();
             }