Configuring STARS on Bio-Linux
Final touches
Customising the gap4 environment
To make gap4 highlight discrepancies between your two strands, and to allow you to make insertions and deletions in the consensus, you can put configuration information in a file called '.gaprc' in your home directory. If this file does not exist create it and add the following lines:
set_def CONTIG_EDITOR.SE_DEL_ANY_CONS 1
set_def CONTIG_EDITOR.SE_INS_CONS 1
set_def CONTIG_EDITOR.DISAGREEMENTS 1
set_def CONTIG_EDITOR.DISAGREE_MODE 3