The very bottom line of the editor display is text line used by the editor to display pieces of useful information. Currently this gives information on individual bases, readings, the contig, and tags, as the mouse is moved over the appropriate object. Each type of object we move the mouse pointer over (sequence base, consensus base, sequence name panel, annotation) has its own list of information to display which can be configured using a format string stored in your $HOME/.gap5rc file.
Typically you will not need to modify these, but if you choose to do so the default values to start from are shown below.
# Mouse-over a sequence the reading name panel set_def READ_BRIEF_FORMAT \ {Reading:%n(#%Rn) Tech:%V Length:%l(%L) MappingQ:%m%**/%*m Pos:%S%p / %*S%*p} # Mouse-over the "Consensus" label in the name panel set_def CONTIG_BRIEF_FORMAT \ {Contig:%n(#%Rn) Length:%l Start:%s End:%e} # Mouse-over a base in a sequence set_def BASE_BRIEF_FORMAT1 \ { Base %b confidence:%4.1c (Prob. %Rc, raw %4.1A %4.1C %4.1G %4.1T) Position %Rp %n} # Mouse-over a base in the consensus set_def BASE_BRIEF_FORMAT2 \ {Base confidence:%4.1c (Prob. %Rc) A=%4.1A C=%4.1C G=%4.1G T=%4.1T *=%4.1* Position %p} # Mouse-over an annotation set_def TAG_BRIEF_FORMAT \ {Tag type:%t Comment:"%.100c"}
The text output is as listed above, but replacing percent-code strings
with a relevant piece of text. In many cases a capital R indicates raw
mode to display a numerical value instead of a string. For example
%n
in READ_BRIEF_FORMAT will be replaced by the sequence name
while %Rn
will be replaced by the sequence record number. The
full syntax of percent expansion is as follows:
To programmers this syntax may seem very similar to printf
. This is
intentional, but do not assume it is the same. Specifically the print syntax
of %#
, %+
and %0
will not work.
Used when we move the mouse over a sequence name in the names panel or a sequence base-call. Example output is Reading:xc04a1.s1(#74) Tech:Sanger Length:295(474) MappingQ:50. Note that not all expansions make sense when used in the names panel as no cursor X position is available.
For the CONTIG_BRIEF_FORMAT and BASE_BRIEF_FORMAT2 the following expansions apply. These operate on contigs and the consensus sequence.
The TAG_BRIEF_FORMAT string is used to display annotation summaries. The possible percent encodings are as follows.