diff --git a/src/main.cpp b/src/main.cpp index fac42c71..f3c86907 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -105,7 +105,7 @@ int main(int argc, char **argv) { {'l', "poa-length-target"}); args::ValueFlag _max_poa_length(poa_opts, "N", "maximum sequence length to put into POA, cut sequences over this length (1k = 1K = 1000, 1m = 1M = 10^6, 1g = 1G = 10^9) [default: 2*poa-length-target = 10k]", {'q', "poa-length-max"}); - args::ValueFlag _poa_padding_fraction(poa_opts, "N", "flanking sequence length fraction (padding = average sequence length in the block * N) to pad each end of each sequence with during POA, in effect overlapping and trimming the POA problems [default: 0.01]", + args::ValueFlag _poa_padding_fraction(poa_opts, "N", "flanking sequence length fraction (padding = average sequence length in the block * N) to pad each end of each sequence with during POA, in effect overlapping and trimming the POA problems [default: 0.001]", {'O', "poa-padding-ratio"}); args::ValueFlag _max_block_depth_for_padding_more(poa_opts, "N", "maximum block depth beyond which a (small) fixed amount of flanking nucleotides is not added (1k = 1K = 1000, 1m = 1M = 10^6, 1g = 1G = 10^9) [default: 1000, 0 to disable it]", @@ -264,7 +264,7 @@ int main(int argc, char **argv) { const uint64_t max_copy_length = _max_copy_length ? (uint64_t)smoothxg::handy_parameter(args::get(_max_copy_length), 20000) : 20000; const uint64_t target_poa_length = _target_poa_length ? (uint64_t)smoothxg::handy_parameter(args::get(_target_poa_length), 5000) : 5000; const uint64_t max_poa_length = _max_poa_length ? (uint64_t)smoothxg::handy_parameter(args::get(_max_poa_length), 2 * target_poa_length) : 2 * target_poa_length; - const float poa_padding_fraction = _poa_padding_fraction ? args::get(_poa_padding_fraction) : (float) 0.01; + const float poa_padding_fraction = _poa_padding_fraction ? args::get(_poa_padding_fraction) : (float) 0.001; const uint64_t max_block_depth_for_padding_more = _max_block_depth_for_padding_more ? (uint64_t)smoothxg::handy_parameter(args::get(_max_block_depth_for_padding_more), 1000) : 1000; diff --git a/src/smooth.cpp b/src/smooth.cpp index 93aceaa7..18a7fb47 100644 --- a/src/smooth.cpp +++ b/src/smooth.cpp @@ -1694,7 +1694,7 @@ odgi::graph_t* smooth_and_lace(const xg::XG &graph, if (block.path_ranges.size() <= max_block_depth_for_padding_more) { // min amount of flanking sequences to add // avoids corner case of padding failure with shallow short blocks - poa_padding = 47; + poa_padding = 311; } // always pad a fraction of our sequence length // note that this can be very short in deep blocks that tend to have many short sequences