UPDATE: Big rewriting of the readsmappers package. It introduce the MapperProcess class.
UPDATE: In the mapper step in local or hadoop mode, the count of the alignments is now done from the stdout of the mapper. It avoid to reread the output SAM file.
UPDATE: For bowtie 1/2 disable streaming mode.
 UPDATE: Many refactoring to avoid duplication code for Bowtie 1/3 ReadsMappers.
UPDATE: In MapperProcess add a getTemporaryDirectory() method.
UPDATE: Remove pairedEnd and fastqFormat from arguments of SequenceReadsMapper.
UPDATE: MapperProcess now takes a SequenceReadsMapper object instead of a mapper name in its constructor.
UPDATE: In MapperProcess, set illegal state with paired-end mode and
streaming mode.
UPDATE: Add Javadoc in MapperProcess
FIX: in constructor, move initialization for temporary files.
FIX: change command line in mode single-read.
FIX: command line for bowtie2.
FIX: In MapperProcess, now use UUID (and new File()) to create temporary
File object instead of FileUtils.createTempFile that create REAL files.
Merge branch 'new_readsmappers' of
/home/sperrin/shares-net/var/git/eoulsan.git/ into new_readsmappers

Conflicts:
	src/main/java/fr/ens/transcriptome/eoulsan/bio/readsmappers/MapperProcess.java
Merge branch 'master' into new_readsmappers
FIX: in FastqCompareFiles.compareNonOrderedFiles(), 2° loop for calls
read2 instead of read1 for make comparaison between us.
UPDATE : generator validator, add panel for genome alias and help.
UPDATE : generator validator, add loading indexes alias from a link or parameter request.
UPDATE: samplesheet validator, load genomes or indexes files
FIX: loading indexes files
Update style for page html.