FIX: in PseudoMapReduce, the reduce method was always called for the
first entry of the sorted file.
CHANGE : 1/ methods for execute process : use class ProcessBuilder of
Java instead of script shell, 2/ in SequenceReadsMapper : signature
methods map() and init().
ADD : class AbstractBowtieReadsMapper for refactor the code of 2
bowtie mappers
FIX : ReadsAlignmentsFilter method
FIX : execute mappers alignment with process builder instance of shell
script and remove in the command line of error and standard output
redirection
ADD : interface SAMParser in bio.readsfilters, used by mapper. Redefine
internalMap() methods : SAMPerser allow to receive output stream of
mapper without using a temporary file.
ADD : internal class ProcessThreadErrOutput to fetch standard error of
the process
ADD : method to create a genome description for SAM file from string
list
FIX : in Readsmapper, modification of the method 'getIndexerCommand', it
return a string list for create the ProcessBuilder command.
ADD javadoc in class eoulsan/bio/readsmappers
ADD : in AbstratBowtieReadsMapper method internalMap, add code for
execute bowtie on paired mode with a SAM parser to get back output
ADD : in FileUtils add method for copy bytes from an InputStream to an
OutputStream without closing the outputStream.
FIX : move class SAMParserLine from package bio.readsfilters to package
bio
FIX: remove old method sort in PseudoMapReduce.
ADD: in LocalEoulsanRuntime, add method for initialization Eoulsan
runtime for external application when use Eoulsan.
FIX: In SAMParser.setGenomeDescription(), now use an HashSet to test
if sequence (chromosome) already exists and no more List.contains().
UPDATE : delete .Rnw script removing step in Rserve mode to keep it in 
results files.
UPDATE: Update Eoulsan documentation.
UPDATE: Update home page of Eoulsan documentation  by adding "RNA-Seq analysis" and "What's new in Eoulsan" sections.
UPDATE : delete remove R script step in runRserveRnwScript method and
runRnwScript method