From 6d4a6debdc25bef93dac0f9fc037f41c87fe3816 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 14 Apr 2014 16:04:29 -0400 Subject: [PATCH] r716: changed -x pbread --- Makefile | 38 -------------------------------------- fastmap.c | 35 +++++++++++++---------------------- main.c | 2 +- 3 files changed, 14 insertions(+), 61 deletions(-) diff --git a/Makefile b/Makefile index 539f273..631af1a 100644 --- a/Makefile +++ b/Makefile @@ -37,41 +37,3 @@ depend: ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c ) # DO NOT DELETE THIS LINE -- make depend depends on it. - -QSufSort.o: QSufSort.h -bamlite.o: bamlite.h malloc_wrap.h -bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h -bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h malloc_wrap.h kseq.h -bwamem.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h -bwamem.o: ksort.h utils.h kbtree.h -bwamem_pair.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h kvec.h -bwamem_pair.o: utils.h ksw.h -bwape.o: bwtaln.h bwt.h kvec.h malloc_wrap.h bntseq.h utils.h bwase.h bwa.h -bwape.o: ksw.h khash.h -bwase.o: bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h malloc_wrap.h -bwase.o: bwa.h ksw.h -bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h malloc_wrap.h kseq.h -bwt.o: utils.h bwt.h kvec.h malloc_wrap.h -bwt_gen.o: QSufSort.h malloc_wrap.h -bwt_lite.o: bwt_lite.h malloc_wrap.h -bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h malloc_wrap.h -bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h -bwtindex.o: bntseq.h bwt.h utils.h malloc_wrap.h -bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h -bwtsw2_aux.o: malloc_wrap.h bwa.h ksw.h kseq.h ksort.h -bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h malloc_wrap.h ksort.h -bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h malloc_wrap.h -bwtsw2_core.o: khash.h ksort.h -bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h -bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h -bwtsw2_pair.o: malloc_wrap.h ksw.h -example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h -fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h -is.o: malloc_wrap.h -kopen.o: malloc_wrap.h -kstring.o: kstring.h malloc_wrap.h -ksw.o: ksw.h malloc_wrap.h -main.o: utils.h -malloc_wrap.o: malloc_wrap.h -pemerge.o: ksw.h kseq.h malloc_wrap.h kstring.h bwa.h bntseq.h bwt.h utils.h -utils.o: utils.h ksort.h malloc_wrap.h kseq.h diff --git a/fastmap.c b/fastmap.c index dd652af..81c0f20 100644 --- a/fastmap.c +++ b/fastmap.c @@ -146,8 +146,8 @@ int main_mem(int argc, char *argv[]) fprintf(stderr, " -L INT[,INT] penalty for 5'- and 3'-end clipping [%d,%d]\n", opt->pen_clip5, opt->pen_clip3); fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n", opt->pen_unpaired); fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overriden [null]\n"); - fprintf(stderr, " pacbio: -k17 -W40 -w200 -c1000 -r10 -A2 -B7 -O2 -E1 -L0\n"); - fprintf(stderr, " pbread: -k13 -W30 -w100 -c1000 -r10 -A1 -B1 -O0 -E1 -N20 -FeaD.01\n"); + fprintf(stderr, " pacbio: -k17 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -L0\n"); + fprintf(stderr, " pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -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"); fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n"); @@ -170,33 +170,24 @@ 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 (!opt0.a) opt->a = 2, opt0.a = 1; + update_a(opt, &opt0); + if (!opt0.o_del) opt->o_del = 2; + if (!opt0.e_del) opt->e_del = 1; + if (!opt0.o_ins) opt->o_ins = 2; + if (!opt0.e_ins) opt->e_ins = 1; + if (!opt0.b) opt->b = 5; + if (!opt0.w) opt->w = 200; if (!opt0.max_occ) opt->max_occ = 1000; 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 (!opt0.a) opt->a = 1, opt0.a = 1; - update_a(opt, &opt0); - if (!opt0.o_del) opt->o_del = 0; - if (!opt0.e_del) opt->e_del = 1; - if (!opt0.o_ins) opt->o_ins = 0; - if (!opt0.e_ins) opt->e_ins = 1; opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG; - if (!opt0.b) opt->b = 1; - if (!opt0.w) opt->w = 100; if (!opt0.min_seed_len) opt->min_seed_len = 13; - if (!opt0.min_chain_weight) opt->min_chain_weight = 30; - if (!opt0.max_chain_extend) opt->max_chain_extend = 20; - if (opt0.drop_ratio == 0.) opt->drop_ratio = .01; + if (!opt0.max_chain_extend) opt->max_chain_extend = 25; + if (opt0.drop_ratio == 0.) opt->drop_ratio = .001; } else { - if (!opt0.a) opt->a = 2, opt0.a = 1; - update_a(opt, &opt0); - if (!opt0.o_del) opt->o_del = 2; - if (!opt0.e_del) opt->e_del = 1; - if (!opt0.o_ins) opt->o_ins = 2; - if (!opt0.e_ins) opt->e_ins = 1; - if (!opt0.b) opt->b = 7; - if (!opt0.w) opt->w = 200; if (!opt0.min_seed_len) opt->min_seed_len = 17; - if (!opt0.min_chain_weight) opt->min_chain_weight = 40; 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 2db22e6..e2f9266 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.8-r707-dirty" +#define PACKAGE_VERSION "0.7.8-r716-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);