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r844: added intra-species contig mapping mode

This commit is contained in:
Heng Li 2014-09-16 10:53:07 -04:00
parent 90518f11e3
commit 92bc6849a3
2 changed files with 12 additions and 7 deletions
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17
fastmap.c
View File

@ -155,8 +155,9 @@ 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\n", opt->pen_unpaired); 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, " -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, " pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 (PacBio reads to ref)\n");
fprintf(stderr, " ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0\n"); fprintf(stderr, " ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0 (Oxford Nanopore 2D-reads to ref)\n");
fprintf(stderr, " intractg: -B9 -O16 -L5 (intra-species contigs to ref)\n");
// fprintf(stderr, " pbread: -k13 -W40 -c1000 -r10 -A1 -B1 -O1 -E1 -N25 -FeaD.001\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, "\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");
@ -182,16 +183,20 @@ 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 || strcmp(mode, "ont2d") == 0) { if (strcmp(mode, "intractg") == 0) {
if (!opt0.a) opt->a = 1, opt0.a = 1; if (!opt0.o_del) opt->o_del = 16;
update_a(opt, &opt0); if (!opt0.o_ins) opt->o_ins = 16;
if (!opt0.b) opt->b = 9;
if (!opt0.pen_clip5) opt->pen_clip5 = 5;
if (!opt0.pen_clip3) opt->pen_clip3 = 5;
} else if (strcmp(mode, "pacbio") == 0 || strcmp(mode, "pbref") == 0 || strcmp(mode, "pbread") == 0 || strcmp(mode, "ont2d") == 0) {
if (!opt0.o_del) opt->o_del = 1; if (!opt0.o_del) opt->o_del = 1;
if (!opt0.e_del) opt->e_del = 1; if (!opt0.e_del) opt->e_del = 1;
if (!opt0.o_ins) opt->o_ins = 1; if (!opt0.o_ins) opt->o_ins = 1;
if (!opt0.e_ins) opt->e_ins = 1; if (!opt0.e_ins) opt->e_ins = 1;
if (!opt0.b) opt->b = 1; if (!opt0.b) opt->b = 1;
if (opt0.split_factor == 0.) opt->split_factor = 10.; if (opt0.split_factor == 0.) opt->split_factor = 10.;
if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) { // pacbio read-to-read setting; NOT working well! if (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; 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.min_chain_weight) opt->min_chain_weight = 40;
if (!opt0.max_occ) opt->max_occ = 1000; if (!opt0.max_occ) opt->max_occ = 1000;

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r843-dirty" #define PACKAGE_VERSION "0.7.10-r844-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);