Feature request: sequencing masking

[a-h-b]

I'd like Vizbin to recognize masked sequences, i.e. ignore small letters. This would be useful to ignore e.g. 16S regions or other regions that obscure kmer profiles.

Usually, the user would supply the already masked sequence, but if you're mega cool, you could include a module that recognizes highly conserved/structural regions and does the masking internally.

[claczny]

Thx for the suggestion.

A fictious example (real sequences would have to be longer of course):

>seq1
AATTCGATTAGaaaaaaaaaaaaaTGCCAGtctctctc
>seq2
tttttttttACGCGATAGATAGCAATTCCGGTTT

In this example, for seq1, aaaaaaaaaaaaaand tctctctc would have to be ignored and k-mers would only be computed for AATTCGATTAGTGCCAG.
For seq2, ttttttttt would have to be ignored and k-mers would only be computed for ACGCGATAGATAGCAATTCCGGTTT.

• Implement switch (GUI and command-line) to enable this function
• Parser module should ignore lower-case letters (i.e., masked subsequence) in sequences if switch is enabled. N.B. This will affect also the size-selection part as sequences might become (potentially much) shorter if masked sequences are ignored.