diff --git a/build.gradle b/build.gradle
new file mode 100644
index 0000000..915e098
--- /dev/null
+++ b/build.gradle
@@ -0,0 +1,29 @@
+group 'com.harmbrugge.bamtools'
+version '1.0-SNAPSHOT'
+
+apply plugin: 'java'
+
+sourceCompatibility = 1.8
+
+repositories {
+    mavenCentral()
+}
+
+dependencies {
+
+    compile group: 'com.github.samtools', name: 'htsjdk', version: '2.6.1'
+    compile group: 'commons-cli', name: 'commons-cli', version: '1.3.1'
+
+    testCompile group: 'junit', name: 'junit', version: '4.11'
+}
+
+jar {
+    manifest {
+        attributes('Main-Class': 'com.harmbrugge.bamtools.Main')
+
+    }
+
+    from {
+        configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }
+    }
+}
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
new file mode 100644
index 0000000..ca78035
Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
new file mode 100644
index 0000000..46e79a6
--- /dev/null
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -0,0 +1,6 @@
+#Wed Sep 07 16:46:41 CEST 2016
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.13-all.zip
diff --git a/gradlew b/gradlew
new file mode 100755
index 0000000..27309d9
--- /dev/null
+++ b/gradlew
@@ -0,0 +1,164 @@
+#!/usr/bin/env bash
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn ( ) {
+    echo "$*"
+}
+
+die ( ) {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+    JAVACMD=`cygpath --unix "$JAVACMD"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
+function splitJvmOpts() {
+    JVM_OPTS=("$@")
+}
+eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
+JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
+
+exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"
diff --git a/gradlew.bat b/gradlew.bat
new file mode 100644
index 0000000..832fdb6
--- /dev/null
+++ b/gradlew.bat
@@ -0,0 +1,90 @@
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windows variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+if "%@eval[2+2]" == "4" goto 4NT_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+goto execute
+
+:4NT_args
+@rem Get arguments from the 4NT Shell from JP Software
+set CMD_LINE_ARGS=%$
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega
diff --git a/settings.gradle b/settings.gradle
new file mode 100644
index 0000000..f08ccbb
--- /dev/null
+++ b/settings.gradle
@@ -0,0 +1,2 @@
+rootProject.name = 'bamPerCell'
+
diff --git a/src/main/java/com.harmbrugge.bamtools/BamFileFlagAdder.java b/src/main/java/com.harmbrugge.bamtools/BamFileFlagAdder.java
new file mode 100644
index 0000000..8b83028
--- /dev/null
+++ b/src/main/java/com.harmbrugge.bamtools/BamFileFlagAdder.java
@@ -0,0 +1,83 @@
+/*
+ * Copyright (c) 2016 Harm Brugge [harmbrugge@gmail.com].
+ * All rights reserved.
+ */
+package com.harmbrugge.bamtools;
+
+import htsjdk.samtools.*;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * @author Harm Brugge
+ * @version 0.0.1
+ */
+public class BamFileFlagAdder {
+
+    private final static String FLAG_NAME = "CB";
+
+    private String outputDir;
+
+    private final Matcher matcher;
+
+    private File[] bamFiles;
+
+
+    public BamFileFlagAdder(Path pathToBamFiles) {
+
+        this.outputDir = pathToBamFiles.getParent() + "/output/";
+        this.matcher = Pattern.compile("_([ATCG]{14})\\.").matcher("");
+
+        File file = pathToBamFiles.toFile();
+
+        bamFiles = file.listFiles(new FilenameFilter() {
+            @Override
+            public boolean accept(File dir, String name) {
+                return name.toLowerCase().endsWith(".bam");
+            }
+        });
+
+    }
+
+    public void start() throws IOException {
+        File file = new File(outputDir);
+        if (!file.exists()) file.mkdirs();
+
+        for (final File bamFile : bamFiles) {
+            convert(bamFile);
+        }
+    }
+
+    private void convert(File bamFile) throws IOException {
+
+        SamReader bamReader = SamReaderFactory.makeDefault().open(bamFile);
+        String barcode = getBarcodeFromFilename(bamFile.getName());
+
+        File outputFile = new File(outputDir + bamFile.getName());
+
+        final SAMFileWriter outputBam = new SAMFileWriterFactory().makeBAMWriter(bamReader.getFileHeader(),
+                false, outputFile);
+
+        for (final SAMRecord bamRecord : bamReader) {
+            bamRecord.setAttribute(FLAG_NAME, barcode);
+            outputBam.addAlignment(bamRecord);
+        }
+
+        outputBam.close();
+        bamReader.close();
+
+    }
+
+    private String getBarcodeFromFilename(String filename) {
+        matcher.reset(filename);
+
+        if (matcher.find()) return matcher.group(1);
+        return null;
+    }
+
+}
diff --git a/src/main/java/com.harmbrugge.bamtools/BamFileSplitter.java b/src/main/java/com.harmbrugge.bamtools/BamFileSplitter.java
new file mode 100644
index 0000000..f1f4770
--- /dev/null
+++ b/src/main/java/com.harmbrugge.bamtools/BamFileSplitter.java
@@ -0,0 +1,176 @@
+/*
+ * Copyright (c) 2016 Harm Brugge [harmbrugge@gmail.com].
+ * All rights reserved.
+ */
+package com.harmbrugge.bamtools;
+
+import htsjdk.samtools.*;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ *
+ * BamFileSplitter splits a BAM files generated in cell-ranger pipeline from 10xGenomics into a file per singe cell.
+ *
+ * Multimappers are removed by reading the GX flag for multiple genes.
+ *
+ *
+ * @author Harm Brugge
+ * @version 0.0.1
+ */
+public class BamFileSplitter {
+
+    private static final String FILE_NAME_PREFIX = "cell_";
+    private static final String EXTENSION = ".bam";
+
+    private final Log logger = LogFactory.getLog(this.getClass());
+    private final Path pathToBarcodeFile;
+    private final String outputDir;
+
+    private int fileCount;
+    private int recordCount;
+    private int withoutBarcodeCount;
+    private int barcodeNotPresentCount;
+
+    private SamReader samReader;
+    private SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
+
+    /**
+     * Map holding a FileWriter for every output BAM.
+     * The key is the barcode of the cell.
+     */
+    private Map<String, SAMFileWriter> outputBams = new HashMap<>();
+
+    public BamFileSplitter(Path pathToBamFile, Path pathToBarcodeFile, Path outputPath) {
+        if (outputPath == null) outputDir = pathToBamFile.getParent() + "/output/";
+        else outputDir = outputPath.toString();
+
+        File file = new File(outputDir);
+        if (!file.exists()) file.mkdirs();
+
+        this.pathToBarcodeFile = pathToBarcodeFile;
+        this.samReader = SamReaderFactory.makeDefault().open(pathToBamFile.toFile());
+    }
+
+    public BamFileSplitter(Path pathToBamFile, Path pathToBarcodeFile) {
+        this(pathToBamFile, pathToBarcodeFile, null);
+    }
+
+    /**
+     * Start the splitting of the BAM file into single cell files.
+     *
+     * @throws IOException if reading or writing to the bam files fails.
+     */
+    public void split() throws IOException {
+        this.populateKeys();
+
+        for (SAMRecord samRecord :samReader) {
+            recordCount++;
+
+            if (isMultimapped(samRecord)) continue;
+
+            Object Umi = samRecord.getAttribute("UR");
+            if (Umi != null) samRecord.setReadName(samRecord.getReadName() + "_" + Umi);
+
+            Object barcodeObject = samRecord.getAttribute("CB");
+            if (barcodeObject != null) {
+                String barcode = barcodeObject.toString();
+
+                if (outputBams.containsKey(barcode)) {
+                    addRecordToBam(barcode, samRecord);
+                } else {
+//                            logger.warn("Barcode not present in barcode file, for record: " + samRecord.toString());
+                    barcodeNotPresentCount++;
+                }
+            } else {
+//                        logger.warn("No barcode found for SAMRecord: " + samRecord.toString());
+                withoutBarcodeCount++;
+            }
+        }
+
+        System.out.println(this.toString());
+
+        closeOutputWriters();
+        samReader.close();
+    }
+
+    private void populateKeys() throws IOException {
+        try (BufferedReader br = new BufferedReader(new FileReader(pathToBarcodeFile.toFile()))) {
+            String barcode = br.readLine();
+
+            while (barcode != null) {
+                outputBams.put(barcode, createBamWriter(barcode));
+
+                barcode = br.readLine();
+            }
+        }
+    }
+
+    private boolean isMultimapped(SAMRecord samRecord) {
+        Object gxTag = samRecord.getAttribute("GX");
+        if (gxTag != null) {
+            int gxCount = String.valueOf(gxTag).split(";").length;
+            if (gxCount > 1) {
+                return true;
+            }
+        }
+        return false;
+    }
+
+    private void addRecordToBam(String barcode, SAMRecord samRecord) {
+        SAMFileWriter outputBam = outputBams.get(barcode);
+
+        outputBam.addAlignment(samRecord);
+    }
+
+    private File createBamFile(String barcode) {
+        fileCount++;
+
+        String filePath = outputDir + "/" + 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");
+
+        samHeader.addReadGroup(readGroup);
+
+        return samHeader;
+    }
+
+    private SAMFileWriter createBamWriter(String barcode) {
+        File bamFile = this.createBamFile(barcode);
+        SAMFileHeader bamHeader = createBamHeader(barcode);
+
+        return writerFactory.makeSAMOrBAMWriter(bamHeader, true, bamFile);
+    }
+
+    private void closeOutputWriters() {
+        for (Map.Entry<String, SAMFileWriter> entry : outputBams.entrySet()) {
+            SAMFileWriter samFileWriter = entry.getValue();
+            samFileWriter.close();
+        }
+    }
+
+    @Override
+    public String toString() {
+        return "BamFileSplitter{" +
+                "fileCount=" + fileCount +
+                ", recordCount=" + recordCount +
+                ", withoutBarcodeCount=" + withoutBarcodeCount +
+                ", barcodeNotPresentCount=" + barcodeNotPresentCount +
+                '}';
+    }
+}
\ No newline at end of file
diff --git a/src/main/java/com.harmbrugge.bamtools/Main.java b/src/main/java/com.harmbrugge.bamtools/Main.java
new file mode 100644
index 0000000..d685561
--- /dev/null
+++ b/src/main/java/com.harmbrugge.bamtools/Main.java
@@ -0,0 +1,82 @@
+/*
+ * Copyright (c) 2016 Harm Brugge [harmbrugge@gmail.com].
+ * All rights reserved.
+ */
+package com.harmbrugge.bamtools;
+
+import org.apache.commons.cli.*;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+/**
+ * Main class for parsing the commandline arguments and initializing BamFileSplitter
+ *
+ * @author Harm Brugge
+ * @version 0.0.1
+ */
+public class Main {
+
+    private void start(String[] args) {
+
+        String pathToBarcode;
+        String pathToBam;
+        Path outputPath = null;
+
+        CommandLineParser parser = new DefaultParser();
+
+        Options options = new Options();
+        options.addOption("s", "split", false, "Input BAM should be split into singe-cell files");
+        options.addOption("a", "adder", false, "Add barcode flag to input BAM files, extracted from filename");
+        options.addOption("c", "samplesheet", false, "Create samplesheet for provided barcode file");
+        options.addOption("i", true, "Input file BAM file or dir");
+        options.addOption("o", true, "Output folder");
+        options.addOption("b", true, "Input file barcode file");
+
+        try {
+            CommandLine line = parser.parse(options, args);
+            if(!line.hasOption("i")) {
+                HelpFormatter formatter = new HelpFormatter();
+                formatter.printHelp("Bam tools", options);
+                System.exit(1);
+            }
+
+            pathToBam = line.getOptionValue("i");
+
+            if (line.hasOption("o")) outputPath = Paths.get(line.getOptionValue("o"));
+
+            if (line.hasOption("s")) {
+                pathToBarcode = line.getOptionValue("b");
+
+                BamFileSplitter bamFileSplitter = new BamFileSplitter(Paths.get(pathToBam), Paths.get(pathToBarcode), outputPath);
+                bamFileSplitter.split();
+                System.out.println(bamFileSplitter);
+
+            } else if (line.hasOption("a")) {
+                BamFileFlagAdder bamFileFlagAdder = new BamFileFlagAdder(Paths.get(pathToBam));
+                bamFileFlagAdder.start();
+            } else if (line.hasOption("c")) {
+                pathToBarcode = line.getOptionValue("b");
+                SampleSheetCreator sampleSheetCreator = new SampleSheetCreator(Paths.get(pathToBarcode));
+
+                if (outputPath == null) outputPath = Paths.get(System.getProperty("user.dir"));
+
+                sampleSheetCreator.createSamplesheet(outputPath);
+            }
+        }
+        catch (ParseException exp) {
+            System.out.println("Parse exception:" + exp.getMessage());
+        } catch (IOException e) {
+            System.out.println("IO exception");
+        }
+
+    }
+
+    public static void main(String [] args) {
+        Main main = new Main();
+        main.start(args);
+    }
+
+
+}
diff --git a/src/main/java/com.harmbrugge.bamtools/ReadCounter.java b/src/main/java/com.harmbrugge.bamtools/ReadCounter.java
new file mode 100644
index 0000000..6c966e6
--- /dev/null
+++ b/src/main/java/com.harmbrugge.bamtools/ReadCounter.java
@@ -0,0 +1,61 @@
+/*
+ * Copyright (c) 2016 Harm Brugge [harmbrugge@gmail.com].
+ * All rights reserved.
+ */
+package com.harmbrugge.bamtools;
+
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+/**
+ * @author Harm Brugge
+ * @version 0.0.1
+ */
+public class ReadCounter {
+
+    private final static String PATH_TO_BAM = "/Volumes/Macintosh HD/Users/harmbrugge/Documents/Stage/Bams/pbmc6k/cells/cell_1036_AGGTTCGATAGACC-1.bam";
+    private int nhGreaterThan1Count;
+    private int gxGreaterThan1Count;
+    private int total;
+
+    private SamReader samReader;
+
+    public ReadCounter(Path pathToBamFile) {
+        this.samReader = SamReaderFactory.makeDefault().open(pathToBamFile.toFile());
+    }
+
+    public void read() {
+        for (final SAMRecord samRecord : samReader) {
+
+            int nhTag = (int) samRecord.getAttribute("NH");
+            if (nhTag > 1) nhGreaterThan1Count++;
+            
+            Object gxTag = samRecord.getAttribute("GX");
+            if (gxTag != null) {
+                int gxCount = String.valueOf(gxTag).split(";").length;
+                if (gxCount > 1) {
+                    gxGreaterThan1Count++;
+                }
+            }
+
+            total++;
+        }
+
+        System.out.println("NH > 1: " + nhGreaterThan1Count);
+        System.out.println("GX > 1: " + gxGreaterThan1Count);
+        System.out.println("Percentage NH > 1: " + ((double) nhGreaterThan1Count / total * 100) );
+        System.out.println("Percentage GX > 1: " + ((double) gxGreaterThan1Count / total * 100) );
+
+    }
+
+    public static void main(String [] args) {
+        ReadCounter readCounter = new ReadCounter(Paths.get(PATH_TO_BAM));
+        readCounter.read();;
+    }
+
+
+}
diff --git a/src/main/java/com.harmbrugge.bamtools/SampleSheetCreator.java b/src/main/java/com.harmbrugge.bamtools/SampleSheetCreator.java
new file mode 100644
index 0000000..f42c924
--- /dev/null
+++ b/src/main/java/com.harmbrugge.bamtools/SampleSheetCreator.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright (c) 2016 Harm Brugge [harmbrugge@gmail.com].
+ * All rights reserved.
+ */
+package com.harmbrugge.bamtools;
+
+import java.io.*;
+import java.nio.file.Path;
+
+/**
+ * @author Harm Brugge
+ * @version 0.0.1
+ */
+public class SampleSheetCreator {
+
+    private static final String PROJECT_NAME = "SingeCell";
+    private static final String FILENAME_PREFIX = "cell_";
+    private static final String EXTENSION = ".bam";
+
+    private static final String SAMPLE_SHEET_FILENAME = "samplesheet.csv";
+
+    private int fileCount;
+
+    private final Path pathToBarcodeFile;
+
+    public SampleSheetCreator(Path pathToBarcodeFile) {
+         this.pathToBarcodeFile = pathToBarcodeFile;
+    }
+
+    public void createSamplesheet(Path outputDir) throws IOException {
+
+        outputDir.toFile().mkdirs();
+        File outputFile = new File(outputDir.toString(), SAMPLE_SHEET_FILENAME);
+        if (!outputFile.exists()) outputFile.createNewFile();
+
+        // project,cellId,bamFile
+        FileWriter fileWriter = new FileWriter(outputFile.getAbsoluteFile());
+        BufferedWriter bw = new BufferedWriter(fileWriter);
+        bw.write("project,cellId,bamFile\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");
+
+                barcode = br.readLine();
+            }
+        }
+
+        bw.close();
+    }
+}