Latest FAST5 support

Added support for Metrichor changes to FAST5 output format.
Added support for multiple analyses in 1 file (i.e.
/Analyses/Basecall_2D_XXX). New option -basecallindex to support it,
but default behaviour is latest (highest numbered analysis).
Moved from using HDF5 command line tool to using HDF5 Java library.
Replaced the NANOOK_SCRIPT_DIR environment variable with a NANOOK_DIR
one and slightly changed installation process.

.gitignore

@@ -2,5 +2,4 @@ build
 build.xml
 manifest.mf
 nbproject
-dist/README.TXT
-dist/NanoOK.jar
+dist/README.TXT 

HDF5License.txt

@@ -0,0 +1,92 @@
+
+Copyright Notice and License Terms for 
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+-----------------------------------------------------------------------------
+
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 2006-2015 by The HDF Group.
+
+NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 1998-2006 by the Board of Trustees of the University of Illinois.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted for any purpose (including commercial purposes) 
+provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, 
+   this list of conditions, and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, 
+   this list of conditions, and the following disclaimer in the documentation 
+   and/or materials provided with the distribution.
+
+3. In addition, redistributions of modified forms of the source or binary 
+   code must carry prominent notices stating that the original code was 
+   changed and the date of the change.
+
+4. All publications or advertising materials mentioning features or use of 
+   this software are asked, but not required, to acknowledge that it was 
+   developed by The HDF Group and by the National Center for Supercomputing 
+   Applications at the University of Illinois at Urbana-Champaign and 
+   credit the contributors.
+
+5. Neither the name of The HDF Group, the name of the University, nor the 
+   name of any Contributor may be used to endorse or promote products derived 
+   from this software without specific prior written permission from 
+   The HDF Group, the University, or the Contributor, respectively.
+
+DISCLAIMER: 
+THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS 
+"AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no 
+event shall The HDF Group or the Contributors be liable for any damages 
+suffered by the users arising out of the use of this software, even if 
+advised of the possibility of such damage. 
+
+-----------------------------------------------------------------------------
+-----------------------------------------------------------------------------
+
+Contributors:   National Center for Supercomputing Applications (NCSA) at 
+the University of Illinois, Fortner Software, Unidata Program Center (netCDF), 
+The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), 
+and Digital Equipment Corporation (DEC).
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the Lawrence Berkeley 
+National Laboratory (LBNL) and the United States Department of Energy 
+under Prime Contract No. DE-AC02-05CH11231.
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the University of 
+California, Lawrence Livermore National Laboratory (UC LLNL).  
+The following statement applies to those portions of the product and must 
+be retained in any redistribution of source code, binaries, documentation, 
+and/or accompanying materials:
+
+   This work was partially produced at the University of California, 
+   Lawrence Livermore National Laboratory (UC LLNL) under contract 
+   no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy 
+   (DOE) and The Regents of the University of California (University) 
+   for the operation of UC LLNL.
+
+   DISCLAIMER: 
+   This work was prepared as an account of work sponsored by an agency of 
+   the United States Government. Neither the United States Government nor 
+   the University of California nor any of their employees, makes any 
+   warranty, express or implied, or assumes any liability or responsibility 
+   for the accuracy, completeness, or usefulness of any information, 
+   apparatus, product, or process disclosed, or represents that its use 
+   would not infringe privately- owned rights. Reference herein to any 
+   specific commercial products, process, or service by trade name, 
+   trademark, manufacturer, or otherwise, does not necessarily constitute 
+   or imply its endorsement, recommendation, or favoring by the United 
+   States Government or the University of California. The views and 
+   opinions of authors expressed herein do not necessarily state or reflect 
+   those of the United States Government or the University of California, 
+   and shall not be used for advertising or product endorsement purposes.
+-----------------------------------------------------------------------------
+
+

bin/nanook

@@ -2,16 +2,20 @@
 
 JAVA_ARGS="-Xmx2048m"
 
-if [ -z "$NANOOK_SCRIPT_DIR" ] ; then
-    echo "Error: You must set NANOOK_SCRIPT_DIR before running."
+if [ -z "$NANOOK_DIR" ] ; then
+    echo "Error: You must set NANOOK_DIR before running."
     exit 1
 fi
 
-JARFILE=${NANOOK_SCRIPT_DIR}/NanoOK.jar
+JARFILE=${NANOOK_DIR}/dist/NanoOK.jar
 
 if [ ! -f ${JARFILE} ] ; then
-    echo "Error: Can't find NanoOK.jar - it needs to be inside the directory pointed to by NANOOK_SCRIPT_DIR which is currently ${NANOOK_SCRIPT_DIR}"
+    echo "Error: Can't find NanoOK.jar - it needs to be inside the dist subdirectory of the directory pointed to by NANOOK_DIR which is currently ${NANOOK_DIR}"
     exit 1
 fi
 
+# If your library path (DYLD_LIBRARY_PATH on MAC) doesn't include HDF5 libraries,
+# you can manually set it here by adding a -Djava.library.path=/path/to/lib/dir
+# to the java command...
+
 exec java ${JAVA_ARGS} -jar ${JARFILE} "$@"

dist/README.TXT

@@ -0,0 +1,32 @@
+========================
+BUILD OUTPUT DESCRIPTION
+========================
+
+When you build an Java application project that has a main class, the IDE
+automatically copies all of the JAR
+files on the projects classpath to your projects dist/lib folder. The IDE
+also adds each of the JAR files to the Class-Path element in the application
+JAR files manifest file (MANIFEST.MF).
+
+To run the project from the command line, go to the dist folder and
+type the following:
+
+java -jar "NanoOK.jar" 
+
+To distribute this project, zip up the dist folder (including the lib folder)
+and distribute the ZIP file.
+
+Notes:
+
+* If two JAR files on the project classpath have the same name, only the first
+JAR file is copied to the lib folder.
+* Only JAR files are copied to the lib folder.
+If the classpath contains other types of files or folders, these files (folders)
+are not copied.
+* If a library on the projects classpath also has a Class-Path element
+specified in the manifest,the content of the Class-Path element has to be on
+the projects runtime path.
+* To set a main class in a standard Java project, right-click the project node
+in the Projects window and choose Properties. Then click Run and enter the
+class name in the Main Class field. Alternatively, you can manually type the
+class name in the manifest Main-Class element.