Editing Modes

The editor operates in two main edit modes - Replace and Insert. Replace allows a character to be replaced by another and Insert allows characters to be inserted. Replace is the default mode. The mode can be changed by pressing the button marked "Insert". The checkbox next to the button will be set (filled by a dark colour) when the mode is "Insert". By default these modes are restricted until the Edit Modes menu is used to change them.

The Edit Modes menu consists of a series of checkboxes and radiobuttons which control which editing options are enabled.

Allow insert in read

Allow del in read

Insertion or deletion within a reading will shift the sequence characters and so will alter their alignment. This is acceptable provided action is taken to correct it, by either shifting the reading or by inserting or deleting a base elsewhere. This functionality is disabled by default and is enabled by checking the appropriate checkbox. Note though that insertion and deletion of bases within the cutoff data will shuffle the cutoff data rather than the reading itself and hence will not break alignment. However this operation still requires the edit mode to be enabled.

Allow insert any in cons

Allow del dash in cons

Allow del any in cons

These operations control the editing actions allowed for the consensus. By default the only operations allowed are insertion and deletion of pads. This is because consensus editing is typically used for removing columns of pads where a single reading has been overcalled. When editing at 100% disagreement, such cases will be dashes in the consensus, so "Allow del dash in cons" enables deletion of both dash and pads. "Allow insert any in cons" and "Allow del any in cons" allow any column to be completely inserted or deleted. These are potentially dangerous actions, however the "Evidence for edits" options can detect such edits.

Allow replace in cons

Replacing a base in the consensus changes all of the bases in readings at this point that disagree with the typed base. The actual edit performed depends upon the "Edit by base type" and "Edit by confidence" radiobuttons.

Allow reading shift

To shift a reading place the cursor at the far left end of the reading. If cutoffs is set this should be the far left end of the cutoff data. Then typing space or delete will move the reading right or left respectively by one position. This operation is disabled by default.

Allow transpose any

Moving pads within a reading is often a useful procedure, and the 'movement' of a pad alone will not break the alignment. For this reason it is possible to move pads around without using insert/delete. Placing the cursor over a pad in a reading and pressing "Control l" or "Control r" will move that pad left or right one base. This operation will not work with the cursor on the consensus. Pad movement is allowed at all times. The selection of "Allow transpose any" allows any pair of adjacent characters to be swapped.

Allow uppercase

A rule often followed by users is to type all modifications in lower case which makes edited characters easier to see. The "Allow uppercase" checkbox controls whether this rule is enforced or not. By default "Allow uppercase" is checked which means that the rule is not enforced.

Edit by base type

Edit by confidence

These two selections are radiobuttons, and are mutually exclusive. They control the outcome when replacing bases in the consensus. When editing the consensus "Edit by base type" changes bases that disagree with the consensus to the base typed. "Edit by confidence" changes the confidence of disagreeing bases to 0. If the consensus quality cutoff value is greater than or equal to zero, characters with an accuracy value of 0 are ignored in the consensus calculation. That is, although the characters still appear in the reading, they are not used to calculate the consensus. In this way it is possible to maintain the original base calls for visual inspection, but get the correct consensus. Note that "Edit by confidence" will not work if the "frequency" consensus algorithm is in use (see section The Consensus Calculation). If you wish to use "Edit by confidence", make sure that the quality cutoff is zero or higher, otherwise the frequency consensus algorithm will be used instead.

Mode set 1

Mode set 2

To make it easier to set the editing modes two user definable sets are available. By default these are as follows. Mode set 1:

• Disallow insert in read
• Disallow del in read
• Disallow insert any in cons
• Allow del dash in cons
• Disallow del any in cons
• Disallow replace in cons
• Disallow reading shift
• Disallow transpose any
• Allow uppercase
• Edit by confidence

Mode set 2:

• Allow insert in read
• Allow del in read
• Allow insert any in cons
• Allow del dash in cons
• Disallow del any in cons
• Allow replace in cons
• Allow reading shift
• Disallow transpose any
• Allow uppercase
• Edit by confidence

Currently the only way of redefining these sets is to add lines to your `.gaprc' file.See section Options Menu. The method is to define a list of 1s and 0s to specify the states in the order listed above. The two default sets are defined as follows.

set_def CONTIG_EDITOR.SE_SET.1    {0 0 0 1 0 0 0 0 1 1}
set_def CONTIG_EDITOR.SE_SET.2    {1 1 1 1 0 1 1 0 1 1}