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r729: halved band width; doubled patch band width

This commit is contained in:
Heng Li 2014-04-24 16:06:01 -04:00
parent 6052d3015b
commit 76bb49e01b
3 changed files with 4 additions and 5 deletions
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2
bwamem.c
View File

@ -376,7 +376,7 @@ int mem_patch_reg(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
if (bwa_verbose >= 4)
printf("* potential hit merge between [%d,%d)<=>[%ld,%ld) and [%d,%d)<=>[%ld,%ld), @ %s; w=%d, r=%.4g\n",
a->qb, a->qe, (long)a->rb, (long)a->re, b->qb, b->qe, (long)b->rb, (long)b->re, bns->anns[a->rid].name, w, r);
if (w > opt->w) return 0; // the bandwidth is too large
if (w > opt->w<<1) return 0; // the bandwidth is too large
if (r >= PATCH_MAX_R_BW) return 0; // relative bandwidth is too large
// global alignment
w += a->w + b->w;

5
fastmap.c
View File

@ -147,8 +147,8 @@ 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 -B5 -O2 -E1 -L0\n");
fprintf(stderr, " pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FeaD.001\n");
fprintf(stderr, " pacbio: -k17 -W40 -c1000 -r10 -A2 -B5 -O2 -E1 -L0\n");
fprintf(stderr, " pbread: -k13 -W40 -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");
@ -178,7 +178,6 @@ int main_mem(int argc, char *argv[])
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;

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r728-dirty"
#define PACKAGE_VERSION "0.7.8-r729-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);