diff --git a/src/subcommand/surject_main.cpp b/src/subcommand/surject_main.cpp index 1ca5fde97c..b24dd30427 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: 300)" << endl + << " -T, --max-tail-len N only align up to N bases of read tails (default: 10000)" << 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 = 300; + size_t max_tail_len = 10000; bool qual_adj = false; bool prune_anchors = false; size_t max_anchors = 200; diff --git a/src/surjector.hpp b/src/surjector.hpp index 40c9b44f5a..685988f187 100644 --- a/src/surjector.hpp +++ b/src/surjector.hpp @@ -110,7 +110,7 @@ using namespace std; int64_t min_splice_repair_length = 250; /// the maximum length of a tail that we will try to align - size_t max_tail_length = std::numeric_limits::max(); + size_t max_tail_length = 10000; /// How big of a graph in bp should we ever try to align against for realigning surjection? size_t max_subgraph_bases = 100 * 1024;