Be more helpful when validating the input database

[marcelm]

igdiscover init validates the input database and checks whether there are duplicate sequences.

The error we get complains only about the first duplicate sequence that it finds, so it is necessary to re-run init in order to fix and find all problems, which is annoying, especially if the GUI is used.

[marcelm]

@NestorVB I am going to fix this such that the input database is automatically repaired.

[marcelm]

It works as follows.

• If a record is empty, it is skipped.
• If a record name occurs more than once, the second record name gets a suffix (_1, _2 etc.).
• If a sequence occurs more than once, occurrences after the first are skipped

This is how it looks when running igdiscover init:

$ igdiscover init --library-name=testing --db=db-with-problems --reads=reads.1.fastq.gz test
INFO: Records 'VH2b' and 'VH2c' contain the same sequence, skipping 'VH2c'
INFO: Record 'empty_sequence' is empty, skipping it.
INFO: Record name 'same_name' occurs more than once, replaced with 'same_name_1'
INFO: Directory test initialized.
INFO: Edit test/igdiscover.yaml, then run "cd test && igdiscover run" to start the analysis