Help/3 Analysis Modules/12 Per Tile Sequence Quality.html

@@ -45,7 +45,7 @@ tiles.
 
 <h2>Failure</h2>
 <p>
-This module will issue a warning if any tile shows a mean Phred
+This module will raise and error if any tile shows a mean Phred
 score more than 5 less than the mean for that base across all
 tiles. 
 </p>

INSTALL.txt

 Installing FastQC
 -------------------
-FastQC is a java application.  In order to run it needs your system to have a suitable
-Java Runtime Environment (JRE) installed.  Before you try to run FastQC you should therefore
-ensure that you have a suitable JRE.  There are a number of different JREs available
-however the ones we have tested are the v1.6-v1.8 JREs from Oracle.  These are available
-for a number of different platforms.
-
-Windows/Linux: Go to java.com - click on Free Java Download - DON'T click the large red button
-but choose the smaller link to "See all java downloads".  Find your operating system and select
-the appropriate offline installer.  If you are using a 64bit operating system (and nearly 
-everyone is these days), then make sure you select the 64bit version of the the installer.
 
-OSX: On newer versions of OSX you need to install the Java Development Kit.  The normal Java
-runtime environment IS NOT enough.  To get this go to java.com, click "Free java download",
-then IGNORE the big red button, and select "See all java downloads", on the next screen select
-"Looking for the JDK?" from the left hand menu and select the link to "JDK downloads" in the
-first paragraph.  You can then click the "Download" button underneath JDK in the page you are
-taken to.  Sorry this is such a pain!
+OSX
+---
+FastQC is distributed as a DMG image file.  Download the image from the project page
+and double click it to open it.  You should see the FastQC application appear in a
+Finder window.  Drag the application from there to wherever you want to install it 
+on your machine.  Once you've copied the application double click it to open it.
+
+FastQC is not a signed application therefore it may initially be blocked by the
+Gatekeeper application.  To avoid this open FastQC by right clicking on the app 
+and selecting open.  This may prompt you to allow it to open.  If it is still 
+blocked go to System Preferences > Security and Privacy and you should see an option
+to allow the application to open.  You only need to do this once and the preference
+should be remembered by OSX.
+
+Windows and Linux
+-----------------
+FastQC is a java application.  In order to run it needs your system to have a suitable
+Java Runtime Environment (JRE) installed.  Before you try to run FastQC you should 
+therefore ensure that you have a suitable JRE.  There are a number of different JREs 
+available however the ones we have tested are the latest Oracle runtime environments 
+and those from the adoptOpenJDK project (https://adoptopenjdk.net/).  You need to 
+download and install a suitable 64-bit JRE and make sure that the java application 
+is in your path (most installers will take care of this for you).
 
+On linux most distributions will have java installed already so you might not need to
+do anything.  If java isn't installed then you can add it by doing:
 
-If you're not sure whether you have java installed then you can test this from a command
-prompt.  To get a command prompt try:
+Ubuntu / Mint: sudo apt install default-jre
 
-Windows: Select Start > Run, and type 'cmd' (no quotes) in the box which appears, press OK
+CentOS / Redhat: sudo yum install java-1.8.0-openjdk
 
-MaxOSX: Run Applications > Utilities > Terminal
+You can check whether java is installed by opening the 'cmd' program on windows, or
+any shell on linux and typing:
 
-Linux: From your applications menu look for an application called 'Terminal' or 'Konsole'.
-Either of these will give you a usable shell.
+java -version
 
-At the command prompt type 'java -version' and press enter.  You should see something like:
+You should see something like:
 
-java version "1.8.0_60"
-Java(TM) SE Runtime Environment (build 1.8.0_60-b27)
-Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)
+>java -version
+openjdk version "11.0.2" 2019-01-15
+OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.2+9)
+OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.2+9, mixed mode)
 
-If you get an error then you don't have java installed.  If the version listed on the first
-line is less than 1.6 then you might have problems running FastQC.
 
 Actually installing FastQC is as simple as unzipping the zip file it comes in into a
 suitable location.  That's it.  Once unzipped it's ready to go.
@@ -59,9 +66,7 @@ Windows: Simply double click on the run_fastqc bat file.  If you want to make a
 shortcut then we've included an icon file in the top level directory so you don't have
 to use the generic bat file icon.
 
-MacOSX: There is an application bundle for MacOSX which you can use to install and run
-FastQC.  Just drag the application from the disk image to your Applications folder (or
-wherever you want to install the program).
+MacOSX: Double click on the FastQC application icon.
 
 Linux:  We have included a wrapper script, called 'fastqc' which is the easiest way to 
 start the program.  The wrapper is in the top level of the FastQC installation.  You 

RELEASE_NOTES.txt

+RELEASE NOTES FOR FastQC v0.11.9
+--------------------------------
+
+This is a bugfix release which resolves some issues with the program;
+
+- We removed the native look and feel from the linux application since
+  it's horribly broken
+  
+- Fixed a hang if a run terminated from an out-of-memory error
+
+- Fixed a corner case where adapters could occasionally be double-counted
+
+- Updated the fast5 parser to account for the newer format multi-read
+  oxford nanopore fast5 files
+  
+- Fixed problems if analysing a completely blank file
+
+
+
 RELEASE NOTES FOR FastQC v0.11.8
 --------------------------------
 

debian/changelog

+fastqc (0.11.9+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12 (routine-update)
+  * Standards-Version: 4.4.1 (routine-update)
+  * Updated patches.
+
+ -- Steffen Moeller <moeller@debian.org>  Sun, 12 Jan 2020 22:40:39 +0100
+
 fastqc (0.11.8+dfsg-2) unstable; urgency=medium
 
   * Team upload.

debian/compat

-11

debian/control

@@ -5,14 +5,14 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Olivier Sallou <osallou@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                javahelper,
                default-jdk,
                ant,
                libhtsjdk-java,
                libjbzip2-java,
                libcommons-math3-java
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/fastqc
 Vcs-Git: https://salsa.debian.org/med-team/fastqc.git
 Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

debian/patches/drop-fast5.patch

@@ -17,7 +17,7 @@ Index: fastqc/fastqc
 ===================================================================
 --- fastqc.orig/fastqc
 +++ fastqc/fastqc
-@@ -74,7 +74,6 @@ my $quiet;
+@@ -97,7 +97,6 @@ my $quiet;
  my $nogroup;
  my $expgroup;
  my $casava;
@@ -25,7 +25,7 @@ Index: fastqc/fastqc
  my $nofilter;
  my $kmer_size;
  my $temp_directory;
-@@ -92,7 +91,6 @@ my $result = GetOptions('version' => \$v
+@@ -114,7 +113,6 @@ my $result = GetOptions('version' => \$v
  						'threads=i' => \$threads,
  						'kmers=i' => \$kmer_size,
  						'casava' => \$casava,
@@ -33,7 +33,7 @@ Index: fastqc/fastqc
  						'nofilter' => \$nofilter,
  						'contaminants=s' => \$contaminant,
  						'adapters=s' => \$adapter,
-@@ -189,10 +187,6 @@ if ($casava) {
+@@ -211,10 +209,6 @@ if ($casava) {
  	push @java_args ,"-Dfastqc.casava=true";		
  }
  
@@ -44,7 +44,7 @@ Index: fastqc/fastqc
  
  if ($nofilter) {
  	push @java_args ,"-Dfastqc.nofilter=true";		
-@@ -326,11 +320,6 @@ DESCRIPTION
+@@ -350,11 +344,6 @@ DESCRIPTION
                      (including being gzipped and ending with .gz) otherwise they
                      won't be grouped together correctly.
                      
@@ -60,7 +60,7 @@ Index: fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java
 ===================================================================
 --- fastqc.orig/uk/ac/babraham/FastQC/Sequence/Fast5File.java
 +++ /dev/null
-@@ -1,107 +0,0 @@
+@@ -1,142 +0,0 @@
 -/**
 - * Copyright Copyright 2010-17 Simon Andrews
 - *
@@ -84,6 +84,8 @@ Index: fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java
 -
 -import java.io.File;
 -import java.io.IOException;
+-import java.util.ArrayList;
+-import java.util.List;
 -
 -import ch.systemsx.cisd.hdf5.HDF5Factory;
 -import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
@@ -92,45 +94,58 @@ Index: fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java
 -
 -	private Sequence nextSequence = null;
 -	private File file;
--
 -	private String name;
+-	private IHDF5SimpleReader reader;
+-	private String [] readPaths = new String[] {""};
 -	
--	protected Fast5File(File file) throws SequenceFormatException, IOException {
--		this.file = file;
--		name = file.getName();
--
--		IHDF5SimpleReader reader = HDF5Factory.openForReading(file);
+-	private int readPathsIndexPosition = 0;
 -	
--		String [] rdfPaths = new String [] {
+-	private String [] rdfPaths = new String [] {
 -			"Analyses/Basecall_2D_000/BaseCalled_template/Fastq",
 -			"Analyses/Basecall_2D_000/BaseCalled_2D/Fastq",
 -			"Analyses/Basecall_1D_000/BaseCalled_template/Fastq",
 -			"Analyses/Basecall_1D_000/BaseCalled_1D/Fastq"
 -	};
 -
--		boolean foundPath = false;
--		for (int r=0;r<rdfPaths.length;r++) {
 -
--				if (reader.exists(rdfPaths[r])) {
 -
--					foundPath = true;
--					String fastq = reader.readString(rdfPaths[r]);
+-	protected Fast5File(File file) throws SequenceFormatException, IOException {
+-		this.file = file;
+-		name = file.getName();
 -
--					String [] sections = fastq.split("\\n");
+-		reader = HDF5Factory.openForReading(file);
 -		
--					if (sections.length != 4) {
--						throw new SequenceFormatException("Didn't get 4 sections from "+fastq);
--					}
+-		// These files have changed structure over time.  Originally they contained
+-		// a single read per file where the base of the heirarchy was the read 
+-		// itself.
+-		//
+-		// Later the files moved to having multiple reads per file.  Now there is
+-		// an additional top level folder per read with the sub-structure being the
+-		// same as it used to be for the individual reads.
+-		//
+-		// We need to account for both of these structures.
+-		
+-		
+-		// See if we can see a bunch of paths starting with "read_" at the top of the
+-		// heirarchy.  If we can then we substitute the read paths for these.
 -		
--					nextSequence = new Sequence(this, sections[1].toUpperCase(),sections[3], sections[0]);
--					break;
+-		List<String> topLevelFolders = reader.getGroupMembers("/");
+-		
+-		List<String> readFolders = new ArrayList<String>();
+-		
+-		for (String folder : topLevelFolders) {
+-			System.err.println("Looking at "+folder);
+-			
+-			if (folder.startsWith("read_")) {
+-				readFolders.add(folder+"/");
 -			}
 -		}
 -		
--		reader.close();
+-		if (readFolders.size() > 0) {
+-			// We have read folders so we'll replace the default readPaths with
+-			// the list we made
 -			
--		if (!foundPath) {
--			throw new SequenceFormatException("No valid fastq paths found in "+file);
+-			readPaths = readFolders.toArray(new String[0]);
 -		}
 -		
 -	}
@@ -140,9 +155,7 @@ Index: fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java
 -	}
 -
 -	public int getPercentComplete() {
--		if (! hasNext()) return 100;
--
--		return 0;		
+-		return (readPathsIndexPosition*100) / readPaths.length;		
 -	}
 -
 -	public boolean isColorspace() {
@@ -150,13 +163,35 @@ Index: fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java
 -	}
 -
 -	public boolean hasNext() {
--		return nextSequence != null;
+-		return readPathsIndexPosition < readPaths.length;
 -	}
 -
 -	public Sequence next() throws SequenceFormatException {
--		Sequence seq = nextSequence;
--		nextSequence = null;
--		return seq;
+-		
+-		for (int r=0;r<rdfPaths.length;r++) {
+-			
+-				if (reader.exists(readPaths[readPathsIndexPosition]+rdfPaths[r])) {
+-		
+-					String fastq = reader.readString(readPaths[readPathsIndexPosition]+rdfPaths[r]);
+-		
+-					String [] sections = fastq.split("\\n");
+-			
+-					if (sections.length != 4) {
+-						throw new SequenceFormatException("Didn't get 4 sections from "+fastq);
+-					}
+-			
+-					Sequence seq = new Sequence(this, sections[1].toUpperCase(),sections[3], sections[0]);
+-					++readPathsIndexPosition;
+-					
+-					if(readPathsIndexPosition >= readPaths.length) {
+-						reader.close();
+-					}
+-					
+-					return(seq);
+-				}
+-		}
+-		
+-		throw new SequenceFormatException("No valid fastq paths found in "+file);
 -	}
 -
 -	public void remove() {

debian/patches/fastqc.patch

@@ -24,8 +24,8 @@ Index: fastqc/fastqc
 +	$ENV{CLASSPATH} .= "$JavaClasspathExtraDir/commons-math3.jar$delimiter$JavaClasspathExtraDir/htsjdk.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar:$RealBin/fastqc.jar";
  }
  
- my @java_args;
-@@ -277,10 +276,10 @@ if (@files or $version or $help) {
+ 
+@@ -301,10 +300,10 @@ if (@files or $version or $help) {
  
  
  if ($java_bin ne 'java') {

fastqc

@@ -45,6 +45,29 @@ else {
 	$ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";
 }
 
+
+# We need to find the java interpreter.  We'll start from the assumption that this
+# is included in the path.
+
+my $java_bin = "java";
+
+# We might have bundled a jre with the installation.  If that's the case then we'll
+# use the interpreter which is bundled in preference to the system one.
+
+# Windows first
+if (-e "$RealBin/jre/bin/java.exe") {
+	$java_bin = "$RealBin/jre/bin/java.exe";
+}
+# Linux
+elsif (-e "$RealBin/jre/bin/java") {
+	$java_bin = "$RealBin/jre/bin/java";
+}
+# OSX
+elsif (-e "$RealBin/jre/Contents/Home/bin/java") {
+	$java_bin = "$RealBin/jre/Contents/Home/bin/java";
+}
+
+
 my @java_args;
 my @files;
 
@@ -79,7 +102,6 @@ my $nano;
 my $nofilter;
 my $kmer_size;
 my $temp_directory;
-my $java_bin = 'java';
 my $min_length;
 
 my $result = GetOptions('version' => \$version,
@@ -234,6 +256,8 @@ if ($format) {
 }
 
 if ($java_bin ne 'java') {
+
+	warn "Java is $java_bin\n";
 #	$java_bin =~ s/\\/\//g;
 	
 	unless (-e $java_bin) {

uk/ac/babraham/FastQC/Analysis/AnalysisRunner.java

@@ -23,6 +23,7 @@ import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 
+import uk.ac.babraham.FastQC.Modules.BasicStats;
 import uk.ac.babraham.FastQC.Modules.QCModule;
 import uk.ac.babraham.FastQC.Sequence.Sequence;
 import uk.ac.babraham.FastQC.Sequence.SequenceFile;
@@ -105,6 +106,18 @@ public class AnalysisRunner implements Runnable {
 			}
 		}
 		
+		// We need to account for their potentially being no sequences
+		// in the file.  In this case the BasicStats module never gets 
+		// the file name so we need to explicitly pass it.
+		
+		if (seqCount == 0) {
+			for (int m=0; m<modules.length; m++) {
+				if (modules[m] instanceof BasicStats) {
+					((BasicStats)modules[m]).setFileName(file.name());
+				}
+			}
+		}
+		
 		i = listeners.iterator();
 		while (i.hasNext()) {
 			i.next().analysisComplete(file,modules);

uk/ac/babraham/FastQC/Analysis/OfflineRunner.java

@@ -120,12 +120,19 @@ public class OfflineRunner implements AnalysisListener {
 			try {
 				processFile(fileGroups[i]);
 			}
+			catch (OutOfMemoryError e) {
+				System.err.println("Ran out of memory for "+fileGroups[i][0]);
+				e.printStackTrace();
+				System.exit(2);
+			}
 			catch (Exception e) {
 				System.err.println("Failed to process "+fileGroups[i][0]);
 				e.printStackTrace();
 				filesRemaining.decrementAndGet();
 				somethingFailed = true;
 			}
+			
+
 		}
 		
 		// We need to hold this class open as otherwise the main method

uk/ac/babraham/FastQC/FastQCApplication.java

@@ -54,7 +54,7 @@ import uk.ac.babraham.FastQC.Utilities.NanoporeBasename;
 
 public class FastQCApplication extends JFrame {	
 	
-	public static final String VERSION = "0.11.8";
+	public static final String VERSION = "0.11.9";
 	
 	private JTabbedPane fileTabs;
 	private WelcomePanel welcomePanel;
@@ -318,8 +318,14 @@ public class FastQCApplication extends JFrame {
 		}
 		
 		else {
+			// Recent java themes for linux are just horribly broken with missing
+			// bits of UI.  We're therefore not going to set a native look if
+			// we're on linux.  See seqmonk bug #95 for details.
+			
 			try {
+				if (! System.getProperty("os.name").toLowerCase().contains("linux")) {
 					UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+				}
 			} catch (Exception e) {}
 			
 	

uk/ac/babraham/FastQC/Graphs/LineGraph.java

@@ -139,7 +139,7 @@ public class LineGraph extends JPanel {
 		
 		
 		// Now draw the data points
-		int baseWidth = (getWidth()-(xOffset+10))/data[0].length;
+		int baseWidth = (getWidth()-(xOffset+10))/Math.max(data[0].length,1); // Math.max is there in case we have no data (no sequences)
 		if (baseWidth<1) baseWidth=1;
 		
 //		System.out.println("Base Width is "+baseWidth);
@@ -184,6 +184,7 @@ public class LineGraph extends JPanel {
 		for (int d=0;d<data.length;d++) {
 			g.setColor(COLOURS[d % COLOURS.length]);
 			
+			if (data[d].length > 0)
 				lastY = getY(data[d][0]);
 			for (int i=1;i<data[d].length;i++) {
 				int thisY = getY(data[d][i]);

uk/ac/babraham/FastQC/Modules/AdapterContent.java

@@ -146,10 +146,13 @@ public class AdapterContent extends AbstractQCModule {
 		// than we've seen before, but also that the last position we could find a hit
 		// is a positive position.
 		
+		// If the sequence is longer than it was then we need to expand the storage in
+		// all of the adapter objects to account for this.
+		
 		if (sequence.getSequence().length() > longestSequence && sequence.getSequence().length() - longestAdapter > 0) {
 			longestSequence = sequence.getSequence().length();
 			for (int a=0;a<adapters.length;a++) {
-				adapters[a].expandLengthTo(longestSequence-longestAdapter);
+				adapters[a].expandLengthTo((longestSequence-longestAdapter)+1);
 			}
 		}
 
@@ -311,9 +314,10 @@ public class AdapterContent extends AbstractQCModule {
 
 		public void incrementCount (int position) {
 
-			if (position >= positions.length) {
-				expandLengthTo(position+1);
-			}
+			// Don't ever check or expand the storage within this
+			// function as it ends up double counting previously
+			// incremented positions.  Rely on the upstream code
+			// having done the expansion correctly already.
 
 			++positions[position];			
 

uk/ac/babraham/FastQC/Modules/BasicStats.java

@@ -84,11 +84,15 @@ public class BasicStats extends AbstractQCModule {
 		return "Basic Statistics";
 	}
 	
-	public void processSequence(Sequence sequence) {
+	public void setFileName (String name) {
+		this.name = name;
+		
+		this.name = this.name.replaceFirst("stdin:", "");
+	}
 
-		if (name == null) name = sequence.file().name();
+	public void processSequence(Sequence sequence) {
 
-		name = name.replaceFirst("stdin:", "");
+		if (name == null) setFileName(sequence.file().name());
 		
 		// If this is a filtered sequence we simply count it and move on.
 		if (sequence.isFiltered()) {

uk/ac/babraham/FastQC/Modules/DuplicationLevel.java

@@ -151,6 +151,7 @@ public class DuplicationLevel extends AbstractQCModule {
 		
 		
 		percentDifferentSeqs = (dedupTotal/rawTotal)*100;
+		if (rawTotal == 0) percentDifferentSeqs = 100;
 		
 	}
 	

uk/ac/babraham/FastQC/Modules/PerTileQualityScores.java

@@ -322,7 +322,7 @@ public class PerTileQualityScores extends AbstractQCModule {
 	public void makeReport(HTMLReportArchive report) throws IOException,XMLStreamException {
 		if (!calculated) getPercentages();
 		
-		writeDefaultImage(report, "per_tile_quality.png", "Per base quality graph", Math.max(800, xLabels.length*15), 600);
+		writeDefaultImage(report, "per_tile_quality.png", "Per tile quality graph", Math.max(800, xLabels.length*15), 600);
 
 		StringBuffer sb = report.dataDocument();
 		sb.append("#Tile\tBase\tMean\n");

uk/ac/babraham/FastQC/Modules/SequenceLengthDistribution.java

@@ -70,6 +70,11 @@ public class SequenceLengthDistribution extends AbstractQCModule {
 			}
 		}
 		
+		// We can get a -1 value for min if there aren't any valid sequences
+		// at all.
+		
+		if (minLen < 0) minLen = 0;
+		
 		// We put one extra category either side of the actual size
 		if (minLen>0) minLen--;
 		maxLen++;
@@ -194,10 +199,13 @@ public class SequenceLengthDistribution extends AbstractQCModule {
 			return false;
 		}
 
-
+		// We might not have any sequences so only check if we do
+		if (lengthCounts.length > 0) {
+			// Empty sequences get us an error
 			if (lengthCounts[0] > 0) {
 				return true;
 			}
+		}
 		return false;
 	}
 

uk/ac/babraham/FastQC/Results/ResultsPanel.java

@@ -124,7 +124,7 @@ public class ResultsPanel extends JPanel implements ListSelectionListener, Analy
 		panels = new JPanel[modules.length];
 		
 		for (int m=0;m<modules.length;m++) {
-			System.err.println("Getting panel for "+modules[m].name()+" with "+modules[m].description());
+//			System.err.println("Getting panel for "+modules[m].name()+" with "+modules[m].description());
 			panels[m] = modules[m].getResultsPanel();
 		}
 		

uk/ac/babraham/FastQC/Sequence/Fast5File.java

@@ -21,6 +21,8 @@ package uk.ac.babraham.FastQC.Sequence;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
 
 import ch.systemsx.cisd.hdf5.HDF5Factory;
 import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
@@ -29,45 +31,58 @@ public class Fast5File implements SequenceFile {
 
 	private Sequence nextSequence = null;
 	private File file;
-
 	private String name;
+	private IHDF5SimpleReader reader;
+	private String [] readPaths = new String[] {""};
 	
-	protected Fast5File(File file) throws SequenceFormatException, IOException {
-		this.file = file;
-		name = file.getName();
-
-		IHDF5SimpleReader reader = HDF5Factory.openForReading(file);
+	private int readPathsIndexPosition = 0;
 	
-		String [] rdfPaths = new String [] {
+	private String [] rdfPaths = new String [] {
 			"Analyses/Basecall_2D_000/BaseCalled_template/Fastq",
 			"Analyses/Basecall_2D_000/BaseCalled_2D/Fastq",
 			"Analyses/Basecall_1D_000/BaseCalled_template/Fastq",
 			"Analyses/Basecall_1D_000/BaseCalled_1D/Fastq"
 	};
 
-		boolean foundPath = false;
-		for (int r=0;r<rdfPaths.length;r++) {
 
-				if (reader.exists(rdfPaths[r])) {
 
-					foundPath = true;
-					String fastq = reader.readString(rdfPaths[r]);
+	protected Fast5File(File file) throws SequenceFormatException, IOException {
+		this.file = file;
+		name = file.getName();
 
-					String [] sections = fastq.split("\\n");
+		reader = HDF5Factory.openForReading(file);
 		
-					if (sections.length != 4) {
-						throw new SequenceFormatException("Didn't get 4 sections from "+fastq);
-					}
+		// These files have changed structure over time.  Originally they contained
+		// a single read per file where the base of the heirarchy was the read 
+		// itself.
+		//
+		// Later the files moved to having multiple reads per file.  Now there is
+		// an additional top level folder per read with the sub-structure being the
+		// same as it used to be for the individual reads.
+		//
+		// We need to account for both of these structures.
+		
+		
+		// See if we can see a bunch of paths starting with "read_" at the top of the
+		// heirarchy.  If we can then we substitute the read paths for these.
 		
-					nextSequence = new Sequence(this, sections[1].toUpperCase(),sections[3], sections[0]);
-					break;
+		List<String> topLevelFolders = reader.getGroupMembers("/");
+		
+		List<String> readFolders = new ArrayList<String>();
+		
+		for (String folder : topLevelFolders) {
+			System.err.println("Looking at "+folder);
+			
+			if (folder.startsWith("read_")) {
+				readFolders.add(folder+"/");
 			}
 		}
 		
-		reader.close();
+		if (readFolders.size() > 0) {
+			// We have read folders so we'll replace the default readPaths with
+			// the list we made
 			
-		if (!foundPath) {
-			throw new SequenceFormatException("No valid fastq paths found in "+file);
+			readPaths = readFolders.toArray(new String[0]);
 		}
 		
 	}
@@ -77,9 +92,7 @@ public class Fast5File implements SequenceFile {
 	}
 
 	public int getPercentComplete() {
-		if (! hasNext()) return 100;
-
-		return 0;		
+		return (readPathsIndexPosition*100) / readPaths.length;		
 	}
 
 	public boolean isColorspace() {
@@ -87,13 +100,35 @@ public class Fast5File implements SequenceFile {
 	}
 
 	public boolean hasNext() {
-		return nextSequence != null;
+		return readPathsIndexPosition < readPaths.length;
 	}
 
 	public Sequence next() throws SequenceFormatException {
-		Sequence seq = nextSequence;
-		nextSequence = null;
-		return seq;
+		
+		for (int r=0;r<rdfPaths.length;r++) {
+			
+				if (reader.exists(readPaths[readPathsIndexPosition]+rdfPaths[r])) {
+		
+					String fastq = reader.readString(readPaths[readPathsIndexPosition]+rdfPaths[r]);
+		
+					String [] sections = fastq.split("\\n");
+			
+					if (sections.length != 4) {
+						throw new SequenceFormatException("Didn't get 4 sections from "+fastq);
+					}
+			
+					Sequence seq = new Sequence(this, sections[1].toUpperCase(),sections[3], sections[0]);
+					++readPathsIndexPosition;
+					
+					if(readPathsIndexPosition >= readPaths.length) {
+						reader.close();
+					}
+					
+					return(seq);
+				}
+		}
+		
+		throw new SequenceFormatException("No valid fastq paths found in "+file);
 	}
 
 	public void remove() {