From ef4624d3fa4ae616637356adcc21e2f5ce613f42 Mon Sep 17 00:00:00 2001 From: Jordan Eizenga Date: Tue, 16 Jul 2024 09:52:03 -0700 Subject: [PATCH] adjust default max tail len --- src/subcommand/surject_main.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/subcommand/surject_main.cpp b/src/subcommand/surject_main.cpp index 1d374912738..1ca5fde97cd 100644 --- a/src/subcommand/surject_main.cpp +++ b/src/subcommand/surject_main.cpp @@ -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 @@ -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;