transeq frame list

[Peter Rice]

David.Bauer at SCHERING.DE wrote:
> 
> transeq -help says that -frame should be a list.
> But if I specify -frame=1,2,3 it crashes with segmentation fault
> and no visible error in the debug file.
> The last message there is that it correctly recognised the frame list.
> It seems frame can only be a character.
> In fact it is OK because there is the F as alias for 1,2,3
> but -help should give the correct type.

Ah, small problem with the English language.

In EMBOSS, a 'list' is a list of values with short names. 'Select' is a
list of values with no short name but with generated numbers (so far only
embossdata uses this type). 'Lists' can take a 'list of values' (1,2,3) if
they allow more than one value to be set. Transeq only allows a maximum of
1.

Frame can be 1, 2, 3, -1, -2, -3, F, R, "Forward" or "Reverse". (Long names
are given for "F" and "R". The long form for "1" is "1").

The simple solution is:

1. Fix the segmentation fault (strangely, it is in a debug messsage call in
processing the list value  - the array element passed in the call does not
exist :-)

2. Change the help message for lists and selects to explain "Choose 1 from
a list of values" or "Choose up to 4 from a list of values".

3. Look again at long names. The long name for "F" is really "Forward three
frames" but if you put this on the command line, the spaces maked it 3
items "Forward", "Three" and "Frames". As lists and selects normally allow
only 1 value, this can change to force 3 values to use the comma, something
like -frame=1,2,3 and to not allow -frame="1 2 3".

Peter

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723