Includes new options for the TE allele frequency estimation step:
--af_flank_interval is used to control the size of 5' and 3' flanking sequence to be used for flank coverage estimation. The default value is 100bp.
--af_flank_offset is used to control the distance between 5' and 3' flanking sequence and TE boundary. The default value is 200bp.
--af_te_interval is used to control the size of 5' and 3' TE sequence to be used for coverage estimation. The default value is None which means the entire TE locus will be used for coverage estimation.
--af_te_offset is used to control the distance between 5' and 3' TE sequence and TE boundary. The default value is 0bp.
Under default mode (without specifying any parameters), TELR would behave the same way as before. I can change the default value for --af_te_interval and --af_te_offset if we can find a set of optimal values for TAF estimation.
If --af_te_interval is provided, TELR would first determine whether te_start + te_offset + af_te_interval < te_end is true. If the result is true, then TELR would calculate 5' TE locus coverage and 3' TE locus coverage separately and return the average value as final TE locus coverage which will be used for TAF compute. If the result is false, then the whole TE locus will be used for coverage estimation and TAF compute.
--af_flank_interval
is used to control the size of 5' and 3' flanking sequence to be used for flank coverage estimation. The default value is 100bp.--af_flank_offset
is used to control the distance between 5' and 3' flanking sequence and TE boundary. The default value is 200bp.--af_te_interval
is used to control the size of 5' and 3' TE sequence to be used for coverage estimation. The default value isNone
which means the entire TE locus will be used for coverage estimation.--af_te_offset
is used to control the distance between 5' and 3' TE sequence and TE boundary. The default value is 0bp.--af_te_interval
and--af_te_offset
if we can find a set of optimal values for TAF estimation.--af_te_interval
is provided, TELR would first determine whetherte_start + te_offset + af_te_interval < te_end
is true. If the result is true, then TELR would calculate 5' TE locus coverage and 3' TE locus coverage separately and return the average value as final TE locus coverage which will be used for TAF compute. If the result is false, then the whole TE locus will be used for coverage estimation and TAF compute.