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adjust default max tail len
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jeizenga committed Jul 16, 2024
1 parent 62a514b commit ef4624d
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions src/subcommand/surject_main.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ void help_surject(char** argv) {
<< " -b, --bam-output write BAM to stdout" << endl
<< " -s, --sam-output write SAM to stdout" << endl
<< " -l, --subpath-local let the multipath mapping surjection produce local (rather than global) alignments" << endl
<< " -T, --max-tail-len N only align up to N bases of read tails (default: 150)" << endl
<< " -T, --max-tail-len N only align up to N bases of read tails (default: 300)" << endl
<< " -P, --prune-low-cplx prune short and low complexity anchors during realignment" << endl
<< " -a, --max-anchors N use no more than N anchors per target path (default: 200)" << endl
<< " -S, --spliced interpret long deletions against paths as spliced alignments" << endl
Expand Down Expand Up @@ -97,7 +97,7 @@ int main_surject(int argc, char** argv) {
int min_splice_length = 20;
size_t watchdog_timeout = 10;
bool subpath_global = true; // force full length alignments in mpmap resolution
size_t max_tail_len = 150;
size_t max_tail_len = 300;
bool qual_adj = false;
bool prune_anchors = false;
size_t max_anchors = 200;
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vg CI tests complete for branch limit-surject-tails. View the full report here.

16 tests passed, 0 tests failed and 0 tests skipped in 17368 seconds

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