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Large fixed POA min overlap #168

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merged 2 commits into from
Jun 15, 2022
Merged

Large fixed POA min overlap #168

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abebfd3
set 311bp min overlap
ekg Jun 15, 2022
f8085bd
adjust default overlap to be very small
ekg Jun 15, 2022
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4 changes: 2 additions & 2 deletions src/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ int main(int argc, char **argv) {
{'l', "poa-length-target"});
args::ValueFlag<std::string> _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<float> _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<float> _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<std::string> _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]",
Expand Down Expand Up @@ -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;

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2 changes: 1 addition & 1 deletion src/smooth.cpp
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Expand Up @@ -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
Expand Down