There are several consequences of using vector_primer files to specify the sequencing vector details. Please read a description of the vector_primer file algorithm in the algorithms section section Algorithms.
Firstly, to get the vector segments of readings marked correctly it is not necessary to include the relevant data in their experiment files.
Secondly, because vector_clip compares all the primer-vector pairs in the primer_vector file it would be inefficient to include very large numbers of records in these files. Instead it would be better to have a master vector_primer file which contained all the combinations used in the lab and then to copy the relevant ones to project specific files.
Thirdly, even though vector_clip can write the PR record (primer type) into the experiment file if it finds a match, gap4 still needs the template name data in order to do read pair analysis.
Finally note that the -V option for vector_clip means that the segments of sequence in the vector_primer file need not be made exactly the right length when the files are created: it matters only that the cloning site is correctly specified and that there is sufficient length of sequence on either side. For example, vector_primer files could be created in which all records included 40 bases from either side of the cloning sites. The -V option allows the alignment to be limited to the segment of sequence closest to the cloning site. For example, -V 20 specifies that at most 20 bases around the cloning site are used.