Version 2.0.0.4
The quantifier.pl now calculates correctly the remaining read counts.
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 10E6.
The --strata option is added to mapping of reads to the miRBase precursors in the quantifier module.
Quantifier is updated so the 5p and 3p annotation for some species is handled correctly.
The quantifier crashed when the file supplied by option -s could not be opened.
The quantifier has now an additional -W option which will cause reads to be added to a precursor in a weighted way.
That means if a read maps to two different precursors each of them will get this particular read only 0.5 times attached.

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.
MirDeep2 is updated so the 5p and 3p annotation for some species is handled correctly when specified an additional -P option.

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.
