From 90518f11e391071c6d4552d7eeca41cf1d199441 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 16 Sep 2014 10:38:15 -0400 Subject: [PATCH] r843: presetting for ONT 2d reads Somewhat working for 1d reads, but not very well --- fastmap.c | 13 ++++++++++--- main.c | 2 +- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/fastmap.c b/fastmap.c index 6cdad68..57c54e7 100644 --- a/fastmap.c +++ b/fastmap.c @@ -156,6 +156,7 @@ int main_mem(int argc, char *argv[]) fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n\n", opt->pen_unpaired); fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overriden [null]\n"); fprintf(stderr, " pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0\n"); + fprintf(stderr, " ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0\n"); // fprintf(stderr, " pbread: -k13 -W40 -c1000 -r10 -A1 -B1 -O1 -E1 -N25 -FeaD.001\n"); fprintf(stderr, "\nInput/output options:\n\n"); fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n"); @@ -181,7 +182,7 @@ int main_mem(int argc, char *argv[]) } if (mode) { - if (strcmp(mode, "pacbio") == 0 || strcmp(mode, "pbref") == 0 || strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) { + if (strcmp(mode, "pacbio") == 0 || strcmp(mode, "pbref") == 0 || strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0 || strcmp(mode, "ont2d") == 0) { if (!opt0.a) opt->a = 1, opt0.a = 1; update_a(opt, &opt0); if (!opt0.o_del) opt->o_del = 1; @@ -190,14 +191,20 @@ int main_mem(int argc, char *argv[]) if (!opt0.e_ins) opt->e_ins = 1; if (!opt0.b) opt->b = 1; if (opt0.split_factor == 0.) opt->split_factor = 10.; - if (!opt0.min_chain_weight) opt->min_chain_weight = 40; - if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) { + if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) { // pacbio read-to-read setting; NOT working well! opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG; + if (!opt0.min_chain_weight) opt->min_chain_weight = 40; if (!opt0.max_occ) opt->max_occ = 1000; if (!opt0.min_seed_len) opt->min_seed_len = 13; if (!opt0.max_chain_extend) opt->max_chain_extend = 25; if (opt0.drop_ratio == 0.) opt->drop_ratio = .001; + } else if (strcmp(mode, "ont2d") == 0) { + if (!opt0.min_chain_weight) opt->min_chain_weight = 20; + if (!opt0.min_seed_len) opt->min_seed_len = 14; + if (!opt0.pen_clip5) opt->pen_clip5 = 0; + if (!opt0.pen_clip3) opt->pen_clip3 = 0; } else { + if (!opt0.min_chain_weight) opt->min_chain_weight = 40; if (!opt0.min_seed_len) opt->min_seed_len = 17; if (!opt0.pen_clip5) opt->pen_clip5 = 0; if (!opt0.pen_clip3) opt->pen_clip3 = 0; diff --git a/main.c b/main.c index 0b09051..25ce9b4 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.10-r830-dirty" +#define PACKAGE_VERSION "0.7.10-r843-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);