From 546352534b1dbc8db6669c92405ef65163e9b7ad Mon Sep 17 00:00:00 2001 From: cjain7 Date: Sat, 1 May 2021 06:38:03 -0400 Subject: [PATCH] decreasing MCAS sampling rate to improve speed --- src/options.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/options.c b/src/options.c index 330f1b2..5c3ae78 100644 --- a/src/options.c +++ b/src/options.c @@ -51,7 +51,7 @@ void mm_mapopt_init(mm_mapopt_t *opt) //prefix settings specific for sv-aware method opt->maxPrefixLength = 16000; - opt->minPrefixLength = opt->suffixSampleOffset = 1000; //reducing these may increase sensitivity & runtime + opt->minPrefixLength = opt->suffixSampleOffset = 2000; //reducing these may increase sensitivity & runtime opt->prefixIncrementFactor = std::pow((opt->maxPrefixLength - 1) * 1.0/ opt->minPrefixLength, 0.5); opt->min_mapq = 5; opt->min_qcov = 0.5; @@ -93,7 +93,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo) } else if (strcmp(preset, "map-pb") == 0) { //hifi io->flag = 0, io->k = 15; mo->maxPrefixLength = mo->stage2_max_gap = 8000; //reduced - mo->suffixSampleOffset = mo->minPrefixLength = 500; //reduced + mo->suffixSampleOffset = mo->minPrefixLength = 1000; //reduced mo->stage2_bw = 1000; //reduced (making it longer could break alignments near long SVs) mo->prefixIncrementFactor = std::pow((mo->maxPrefixLength - 1) * 1.0/ mo->minPrefixLength, 0.33); //inc. levels } else if (strcmp(preset, "map-pb-clr") == 0) {