The following are used as answers to the initial questions.
fofn file_type do_qual_clip qual_clip_interactive screen_sv SF or SF_com SC or SC_com SP or SP_com screen_cv CF or CF_com screen_av tag_alu
The following are used for default answers to the initial questions. These are only used when the associated question answer is not set.
fofn_def file_type_def do_qual_clip_def qual_clip_interactive_def screen_sv_def SF_def SC_def SP_def screen_cv_def CF_def screen_av_def tag_alu_def
These define the locations for the programs used. They have sensible default values in the pregap script itself and so are not required to be set.
makeSCF eba init_exp (+ exp_args) clip (+ clip_args) vepe repe trev (+ trev_args) getABISampleName
The following define the the parameters used for usually interactive programs, such as vepe and repe.
vepe_svec_word_length vepe_svec_diagonal vepe_svec_score vepe_cvec_word_length vepe_cvec_diagonal vepe_cvec_score vepe_avec_min_match repe_repeat_file repe_score repe_tag_type
Used for determining the file names for the SCF and Experiment files to be created.
abi_SCF_com alf_SCF_com abi_Exp_com alf_Exp_com pln_Exp_com scf_Exp_com abi_Ent_com alf_Ent_com pln_Ent_com scf_Ent_com
Experiment file variables and their associated query commands. The following four are required for use by vepe. (The first three for sequence clipping, the fourth for cosmid vector clipping). See the file $STADENROOT/doc/ExperimentFile.format for descriptions of the two letter identifiers.
SF SF_com SC SC_com SP SP_com CF CF_com
The following are not required, but will be added to the Experiment file during the Augment Experiment File stage if they exist. See the file $STADENROOT/doc/ExperimentFile.format for descriptions of the two letter identifiers.
CN CN_com CV CV_com SV SV_com DR DR_com DT DT_com MC MC_com MN MN_com OP OP_com TN TN_com ST ST_com PN PN_com PR PR_com SI SI_com SS SS_com EX EX_com