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r716: changed -x pbread

This commit is contained in:
Heng Li 2014-04-14 16:04:29 -04:00
parent 1209f161c9
commit 6d4a6debdc
3 changed files with 14 additions and 61 deletions
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38
Makefile
View File

@ -37,41 +37,3 @@ depend:
( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c ) ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )
# DO NOT DELETE THIS LINE -- make depend depends on it. # 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

35
fastmap.c
View File

@ -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, " -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, " -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, " -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, " pacbio: -k17 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -L0\n");
fprintf(stderr, " pbread: -k13 -W30 -w100 -c1000 -r10 -A1 -B1 -O0 -E1 -N20 -FeaD.01\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, "\nInput/output options:\n\n");
fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\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"); 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 (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) {
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.max_occ) opt->max_occ = 1000;
if (opt0.split_factor == 0.) opt->split_factor = 10.; 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) {
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; 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_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 = 25;
if (!opt0.max_chain_extend) opt->max_chain_extend = 20; if (opt0.drop_ratio == 0.) opt->drop_ratio = .001;
if (opt0.drop_ratio == 0.) opt->drop_ratio = .01;
} else { } 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_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_clip5) opt->pen_clip5 = 0;
if (!opt0.pen_clip3) opt->pen_clip3 = 0; if (!opt0.pen_clip3) opt->pen_clip3 = 0;
} }

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r707-dirty" #define PACKAGE_VERSION "0.7.8-r716-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);