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The Editor Information Line

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.

Reading Information

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.

%%
A single % sign
%n
Reading name. Raw mode: record number
%#
Reading record number
%p
Position in sequence. Raw mode: position in contig.
%l
Clipped sequence length
%L
Unclipped sequence length
%s
Start of clip
%e
End of clip
%S
Sense (whether complemented) - "<<" or ">>". Raw mode: 0/1
%d
Strand - "+" or "-". Raw mode: 0/1
%b
Base call
%c
Confidence value of called base (phred style). Raw mode: probability
%A
%C
%G
%T
Individual confidence (phred style) of A,C,G,T component in log-odds form. Raw mode: probability value.
%m
Mapping Quality. Raw mode: probability of correctly mapped.
%V
Instrument type - Sanger, Illumina, SOLiD, 454 or Unknown.

Contig Information

For the CONTIG_BRIEF_FORMAT and BASE_BRIEF_FORMAT2 the following expansions apply. These operate on contigs and the consensus sequence.

%%
Single % sign
%n
Contig name. Raw mode: contig record number.
%#
Contig record number
%p
Position in contig
%l
Length of contig
%s
Contig start coordinate
%e
Contig end coordinate
%b
Called consensus base
%c
Score for called consensus base. Raw mode: probability value
%A
%C
%G
%T
%*
Individual confidence for A,C,G,T,* base types in log-odds form. Raw mode: as a probability value.

Tag Information

The TAG_BRIEF_FORMAT string is used to display annotation summaries. The possible percent encodings are as follows.

%%
Single % sign
%p
Tag position
%t
Tag type (always 4 characters)
%l
Tag length
%#
Tag number (0 if unknown)
%c
Tag comment

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Last generated on 25 November 2011.