8000 query padding by ekg · Pull Request #339 · waveygang/wfmash · GitHub
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query padding #339

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Merged
merged 5 commits into from
Mar 30, 2025
Merged

query padding #339

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c26dc85
feat: Add query padding option for extending mapping boundaries
ekg Mar 29, 2025
b6a6385
feat: Add query padding option to CLI with `-U` or `--query-padding`
ekg Mar 29, 2025
fcdd58a
Revert "refactor: Update progress bar logic to check stdout redirection"
ekg Mar 29, 2025
d28ecd9
feat: Update default WFA alignment parameters to 5,8,2,24,1
ekg Mar 29, 2025
befb8cc
feat: Update query and target padding defaults to 500bp with segment …
ekg Mar 30, 2025
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1 change: 1 addition & 0 deletions src/align/include/align_parameters.hpp
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Expand Up @@ -64,6 +64,7 @@ struct Parameters {
bool disable_chain_patching; //Disable alignment patching at chain boundaries
bool multithread_fasta_input; //Multithreaded fasta input
uint64_t target_padding; //Additional padding around target sequence
uint64_t query_padding; //Additional padding around query sequence

#ifdef WFA_PNG_TSV_TIMING
// plotting
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29 changes: 25 additions & 4 deletions src/align/include/computeAlignments.hpp
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Expand Up @@ -197,7 +197,7 @@ struct seq_record_t {
* @param[in] mappingRecordLine
* @param[out] currentRecord
*/
inline static void parseMashmapRow(const std::string &mappingRecordLine, MappingBoundaryRow &currentRecord, const uint64_t target_padding) {
inline static void parseMashmapRow(const std::string &mappingRecordLine, MappingBoundaryRow &currentRecord, const uint64_t target_padding, const uint64_t query_padding = 0) {
auto tokens = tokenize_view(mappingRecordLine);

// Check if the number of tokens is at least 13
Expand Down Expand Up @@ -241,11 +241,14 @@ struct seq_record_t {
currentRecord.chain_length = chain_length;
currentRecord.chain_pos = chain_pos;

// Apply target padding while ensuring we don't go below 0 or above reference length
// Parse position values
uint64_t rStartPos = std::stoi(std::string(tokens[7]));
uint64_t rEndPos = std::stoi(std::string(tokens[8]));
uint64_t qStartPos = currentRecord.qStartPos;
uint64_t qEndPos = currentRecord.qEndPos;
const uint64_t query_len = std::stoull(std::string(tokens[1])); // Query sequence length

// Always apply target padding
// Apply target padding while ensuring we don't go below 0 or above reference length
if (target_padding > 0) {
if (rStartPos >= target_padding) {
rStartPos -= target_padding;
Expand All @@ -258,6 +261,24 @@ struct seq_record_t {
rEndPos = ref_len;
}
}

// Apply query padding while ensurin 8000 g we don't go below 0 or above query length
if (query_padding > 0) {
if (qStartPos >= query_padding) {
qStartPos -= query_padding;
} else {
qStartPos = 0;
}
if (qEndPos + query_padding <= query_len) {
qEndPos += query_padding;
} else {
qEndPos = query_len;
}

// Update the query positions
currentRecord.qStartPos = qStartPos;
currentRecord.qEndPos = qEndPos;
}

// Validate coordinates against reference length
if (rStartPos >= ref_len || rEndPos > ref_len) {
Expand Down Expand Up @@ -403,7 +424,7 @@ void processMappingRecord(
try {
// Parse the mapping record
MappingBoundaryRow currentRecord;
parseMashmapRow(record, currentRecord, param.target_padding);
parseMashmapRow(record, currentRecord, param.target_padding, param.query_padding);

// Create sequence record
std::unique_ptr<seq_record_t> seq_rec(
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4 changes: 2 additions & 2 deletions src/common/progress.hpp
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Expand Up @@ -103,8 +103,8 @@ class ProgressMeter {
start_time = std::chrono::high_resolution_clock::now();
last_file_update = start_time;

// Check if stderr is a TTY *AND* stdout is not redirected to a file
use_progress_bar = isatty(fileno(stderr)) && isatty(fileno(stdout));
// Check if stderr is a TTY
use_progress_bar = isatty(fileno(stderr));

// For file output, print initial banner with 0% progress
if (!use_progress_bar) {
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24 changes: 19 additions & 5 deletions src/interface/parse_args.hpp
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Expand Up @@ -126,7 +126,8 @@ void parse_args(int argc,

args::Group alignment_opts(options_group, "Alignment:");
args::ValueFlag<std::string> input_mapping(alignment_opts, "FILE", "input PAF file for alignment", {'i', "align-paf"});
args::ValueFlag<std::string> target_padding(alignment_opts, "INT", "padding around target sequence [100]", {'E', "target-padding"});
args::ValueFlag<std::string> target_padding(alignment_opts, "INT", "padding around target sequence [500]", {'E', "target-padding"});
args::ValueFlag<std::string> query_padding(alignment_opts, "INT", "padding around query sequence [500]", {'U', "query-padding"});
args::ValueFlag<std::string&g 8000 t; wfa_params(alignment_opts, "vals",
"scoring: mismatch, gap1(o,e), gap2(o,e) [6,6,3,24,1]", {'g', "wfa-params"});
args::Flag disable_chain_patching(alignment_opts, "", "disable alignment patching at chain boundaries", {"disable-chain-patching"});
Expand Down Expand Up @@ -293,9 +294,9 @@ void parse_args(int argc,
align_parameters.wfa_patching_gap_opening_score2 = params[3];
align_parameters.wfa_patching_gap_extension_score2 = params[4];
} else {
align_parameters.wfa_patching_mismatch_score = 6;
align_parameters.wfa_patching_gap_opening_score1 = 6;
align_parameters.wfa_patching_gap_extension_score1 = 3;
align_parameters.wfa_patching_mismatch_score = 5;
align_parameters.wfa_patching_gap_opening_score1 = 8;
align_parameters.wfa_patching_gap_extension_score1 = 2;
align_parameters.wfa_patching_gap_opening_score2 = 24;
align_parameters.wfa_patching_gap_extension_score2 = 1;
}
Expand Down Expand Up @@ -533,7 +534,20 @@ void parse_args(int argc,
}
align_parameters.target_padding = p;
} else {
align_parameters.target_padding = 100;
// Default to half segment length, capped at 5000
align_parameters.target_padding = std::min(map_parameters.segLength / 2, (int64_t)5000);
}

if (query_padding) {
const int64_t p = handy_parameter(args::get(query_padding));
if (p < 0) {
std::cerr << "[wfmash] ERROR: query padding must be >= 0" << std::endl;
exit(1);
}
align_parameters.query_padding = p;
} else {
// Default to half segment length, capped at 5000
align_parameters.query_padding = std::min(map_parameters.segLength / 2, (int64_t)5000);
}

if (thread_count) {
Expand Down
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