r716: changed -x pbread
This commit is contained in:
Heng Li
parent
1209f161c9
commit
6d4a6debdc
38
Makefile
38
Makefile
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@ -37,41 +37,3 @@ depend:
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( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )
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# DO NOT DELETE THIS LINE -- make depend depends on it.
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QSufSort.o: QSufSort.h
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bamlite.o: bamlite.h malloc_wrap.h
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bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h
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bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h malloc_wrap.h kseq.h
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bwamem.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h
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bwamem.o: ksort.h utils.h kbtree.h
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bwamem_pair.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h kvec.h
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bwamem_pair.o: utils.h ksw.h
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bwape.o: bwtaln.h bwt.h kvec.h malloc_wrap.h bntseq.h utils.h bwase.h bwa.h
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bwape.o: ksw.h khash.h
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bwase.o: bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h malloc_wrap.h
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bwase.o: bwa.h ksw.h
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bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h malloc_wrap.h kseq.h
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bwt.o: utils.h bwt.h kvec.h malloc_wrap.h
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bwt_gen.o: QSufSort.h malloc_wrap.h
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bwt_lite.o: bwt_lite.h malloc_wrap.h
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bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h malloc_wrap.h
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bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h
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bwtindex.o: bntseq.h bwt.h utils.h malloc_wrap.h
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bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h
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bwtsw2_aux.o: malloc_wrap.h bwa.h ksw.h kseq.h ksort.h
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bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h malloc_wrap.h ksort.h
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bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h malloc_wrap.h
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bwtsw2_core.o: khash.h ksort.h
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bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h
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bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h
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bwtsw2_pair.o: malloc_wrap.h ksw.h
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example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h
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fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h
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is.o: malloc_wrap.h
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kopen.o: malloc_wrap.h
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kstring.o: kstring.h malloc_wrap.h
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ksw.o: ksw.h malloc_wrap.h
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main.o: utils.h
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malloc_wrap.o: malloc_wrap.h
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pemerge.o: ksw.h kseq.h malloc_wrap.h kstring.h bwa.h bntseq.h bwt.h utils.h
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utils.o: utils.h ksort.h malloc_wrap.h kseq.h
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33
fastmap.c
33
fastmap.c
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@ -146,8 +146,8 @@ int main_mem(int argc, char *argv[])
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fprintf(stderr, " -L INT[,INT] penalty for 5'- and 3'-end clipping [%d,%d]\n", opt->pen_clip5, opt->pen_clip3);
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fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n", opt->pen_unpaired);
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fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overriden [null]\n");
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fprintf(stderr, " pacbio: -k17 -W40 -w200 -c1000 -r10 -A2 -B7 -O2 -E1 -L0\n");
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fprintf(stderr, " pbread: -k13 -W30 -w100 -c1000 -r10 -A1 -B1 -O0 -E1 -N20 -FeaD.01\n");
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fprintf(stderr, " pacbio: -k17 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -L0\n");
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fprintf(stderr, " pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FeaD.001\n");
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fprintf(stderr, "\nInput/output options:\n\n");
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fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n");
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fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
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@ -170,33 +170,24 @@ int main_mem(int argc, char *argv[])
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if (mode) {
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if (strcmp(mode, "pacbio") == 0 || strcmp(mode, "pbref") == 0 || strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) {
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if (!opt0.max_occ) opt->max_occ = 1000;
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if (opt0.split_factor == 0.) opt->split_factor = 10.;
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if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) {
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if (!opt0.a) opt->a = 1, opt0.a = 1;
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update_a(opt, &opt0);
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if (!opt0.o_del) opt->o_del = 0;
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if (!opt0.e_del) opt->e_del = 1;
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if (!opt0.o_ins) opt->o_ins = 0;
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if (!opt0.e_ins) opt->e_ins = 1;
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opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG;
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if (!opt0.b) opt->b = 1;
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if (!opt0.w) opt->w = 100;
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if (!opt0.min_seed_len) opt->min_seed_len = 13;
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if (!opt0.min_chain_weight) opt->min_chain_weight = 30;
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if (!opt0.max_chain_extend) opt->max_chain_extend = 20;
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if (opt0.drop_ratio == 0.) opt->drop_ratio = .01;
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} else {
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if (!opt0.a) opt->a = 2, opt0.a = 1;
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update_a(opt, &opt0);
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if (!opt0.o_del) opt->o_del = 2;
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if (!opt0.e_del) opt->e_del = 1;
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if (!opt0.o_ins) opt->o_ins = 2;
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if (!opt0.e_ins) opt->e_ins = 1;
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if (!opt0.b) opt->b = 7;
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if (!opt0.b) opt->b = 5;
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if (!opt0.w) opt->w = 200;
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if (!opt0.min_seed_len) opt->min_seed_len = 17;
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if (!opt0.max_occ) opt->max_occ = 1000;
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if (opt0.split_factor == 0.) opt->split_factor = 10.;
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if (!opt0.min_chain_weight) opt->min_chain_weight = 40;
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if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) {
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opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG;
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if (!opt0.min_seed_len) opt->min_seed_len = 13;
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if (!opt0.max_chain_extend) opt->max_chain_extend = 25;
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if (opt0.drop_ratio == 0.) opt->drop_ratio = .001;
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} else {
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if (!opt0.min_seed_len) opt->min_seed_len = 17;
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if (!opt0.pen_clip5) opt->pen_clip5 = 0;
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if (!opt0.pen_clip3) opt->pen_clip3 = 0;
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}
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