Version 2.0.0.8
The install.pl script has been updated to download automatically the latest PDF::API2 version and the latest bowtie1 version.
Source code has been cleaned up and pathes have been adapted. So when using this version please do a new installation of miRDeep2 
and do not just copy scripts over old version. Otherwise your installation will likely be broken.
RNAfold and randfold now compile again on MacOSX 10.10.5 due to adaptation of the fold.c source file in these packages.
minor issues removed
code is cleaned up and installation directories are also organzied more reasonable
Sean Eddys squid libray is included in the package already since the download server is sometimes not to be working 



Version 2.0.0.6
corrected bed file coordinates, off by one error fixed
the zebrafish switch works now in the species specification
novel detected miRNA sequences by the miRDeep2 module are now stored in separate files
in the mapper module all tmp files are deleted now when the specific option is given
install.pl script has been updated in regards of program download links
additional file checks were included for the mapper module when using options a,b,c or e
novel detected miRNA sequences and bed coordinates are output automatically now

Version 2.0.0.5
The quantifier.pl has a new switch '-U' that causes the usage of only uniquely mapping reads to reference precursors.
The mapper.pl reports now the number and percentage of mapped and unmapped reads from the collapsed reads file to a reference genome.
miRDeep2 now aborts now when no precursors were excised.
A bed file of all miRDeep2 detected precursors is created in the end.
An additional check of the arf file ids and genome file ids was added to make sure that ids in both files really match.
An additional check for the presence of the Rfam indices was added.
A bug was fixed that occurred when the miRDNA ids were too long.
The html file in the end does not abort anymore when the Rfam index is missing.


Version 2.0.0.4
The quantifier.pl now calculates correctly the remaining read counts.
Reads that map to more than one precursor are now added in a weighed way
to each precursor. The normalization of read counts in the quantifier.pl
has changed a bit. Each miRNA read count is now divided by the total number of sequenced miRNA read counts and then multiplied by 10E9.
The --strata option is added to mapping of reads to the miRBase precursors in the quantifier module.

The miRDeep2 html output has been updated so that for known miRNAs
the field 'mature miRBase miRNA' now contains the miRNA that matches
the predicted mature sequence or in case that the predicted star
sequence matches a known miRNA this is then shown instead.

The install.pl script can also use curl if wget is not available on the machine.
This is useful for MACOSX users.

The mapper.pl now also determines the number of cores on Mac machines correctly.

A bug has been fixed in the prepare_signature.pl file. It crashed when no known_mature_mirna file was supplied.

RNAfold2 can be used as well now if already installed. Otherwise version 1.8.4 of the Vienna package is downloaded when running the install.pl script.
