1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
|
Ideas/To Do
-----------
This is a rather unsorted list of features that would be nice to have, of
things that could be improved in the source code, and of possible algorithmic
improvements.
- show average error rate
- length histogram
- ``--detect`` prints out best guess which of the given adapters is the correct one
- warn when given adapter sequence contains non-IUPAC characters
Specifying adapters
~~~~~~~~~~~~~~~~~~~
Allow something such as ``-a ADAP$TER`` or ``-a ADAPTER$NNN``.
This would be a way to specify less strict anchoring.
Allow ``N{3,10}`` as in regular expressions (for a variable-length sequence).
Use parentheses to specify the part of the sequence that should be kept:
* ``-a (...)ADAPTER`` (default)
* ``-a (...ADAPTER)`` (default)
* ``-a ADAPTER(...)`` (default)
* ``-a (ADAPTER...)`` (??)
Or, specify the part that should be removed:
``-a ...(ADAPTER...)``
``-a ...ADAPTER(...)``
``-a (ADAPTER)...``
Available letters for command-line options
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Lowercase letters: i, k, s, w
* Uppercase letters: C, D, E, F, H, I, J, K, L, P, R, S, T, V, W
* Deprecated, could be re-used: c, d, t
* Planned/reserved: Q (paired-end quality trimming), V (alias for --version)
|
