Collects observations. log activity and meeting minutes.


Former-commit-id: 67ea01551c5e0c3a1fbb6518b88b188fb52fa93b
Moved notes to doc dir.


Former-commit-id: 0aa579743e9ee5c8466e65bad8540ba66507deb7
Work done so far for BLAST parser.


Former-commit-id: b748cd868b3c5d904cbfa96ac90012b2f732e4ee
Merged with master
Initial implementation of blast_formatter parser module.
Minimal parameter checking.
Checking the specified blast_formatter output format.
We support only the tabular, tabular with comment lines and the CSV.

Removed check on filename, parent classes do not support it.
Tests of the blast_formatter parser. Initial implementation.
Documentation on how to get the input files for the BLAST parser tests.
An input file (tabular, no comment lines) to test the BLAST parser.
An input file (tabular with comment lines, default format specifiers) to test the BLAST parser.
An input file (tabular with comment lines, format specifiers used by Compara) to test the BLAST parser.
An input file (comma-separated values, default format specifiers) to test the BLAST parser.
Decided to introduce file error checking at this level, as there's no checking upstream in the hierarchy.
Forgot using Ensembl throw.
Testing invalid arguments exception handling.
Delimiter is set according to the format specifier.
Test parsing of format specifiers from output format argument.
Method "open": parse output format correctly to set alignment view and format specifier options to base class constructor.
Added method mandatory method set_fields which sets the fields according to the format specifier parameter.
Allows more arbitrary format specifications.
Calling the method set_fields should already assigns $self->{fields}, so it is redundant to
reassign it by calling the method.
Moreover, it could be dangerous in case the method set_fields do not contain as the last instruction
the assignment of $self->{fields}, as this will be assigned to whatever the last expression of
set_fields is evaluated to.