zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

r434: added the missing bwasw/aln commands!

This commit is contained in:
Heng Li 2014-02-12 15:39:02 -05:00
parent 7c50bad567
commit 14aa43cca0
1 changed files with 21 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

22
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.6a-r433" #define PACKAGE_VERSION "0.7.6a-dev-r434"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);
@ -14,9 +14,17 @@ int bwa_bwt2sa(int argc, char *argv[]);
int bwa_index(int argc, char *argv[]); int bwa_index(int argc, char *argv[]);
int bwt_bwtgen_main(int argc, char *argv[]); int bwt_bwtgen_main(int argc, char *argv[]);
int bwa_aln(int argc, char *argv[]);
int bwa_sai2sam_se(int argc, char *argv[]);
int bwa_sai2sam_pe(int argc, char *argv[]);
int bwa_bwtsw2(int argc, char *argv[]);
int main_fastmap(int argc, char *argv[]); int main_fastmap(int argc, char *argv[]);
int main_mem(int argc, char *argv[]); int main_mem(int argc, char *argv[]);
int main_pemerge(int argc, char *argv[]);
char *bwa_pg; char *bwa_pg;
static int usage() static int usage()
@ -29,6 +37,11 @@ static int usage()
fprintf(stderr, "Command: index index sequences in the FASTA format\n"); fprintf(stderr, "Command: index index sequences in the FASTA format\n");
fprintf(stderr, " mem BWA-MEM algorithm\n"); fprintf(stderr, " mem BWA-MEM algorithm\n");
fprintf(stderr, " fastmap identify super-maximal exact matches\n"); fprintf(stderr, " fastmap identify super-maximal exact matches\n");
fprintf(stderr, " pemerge merge overlapping paired ends (EXPERIMENTAL)\n");
fprintf(stderr, " aln gapped/ungapped alignment\n");
fprintf(stderr, " samse generate alignment (single ended)\n");
fprintf(stderr, " sampe generate alignment (paired ended)\n");
fprintf(stderr, " bwasw BWA-SW for long queries\n");
fprintf(stderr, "\n"); fprintf(stderr, "\n");
fprintf(stderr, " fa2pac convert FASTA to PAC format\n"); fprintf(stderr, " fa2pac convert FASTA to PAC format\n");
fprintf(stderr, " pac2bwt generate BWT from PAC\n"); fprintf(stderr, " pac2bwt generate BWT from PAC\n");
@ -60,8 +73,15 @@ int main(int argc, char *argv[])
else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1); else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1);
else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1); else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1);
else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1); else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1);
else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1);
else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1);
else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1);
else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1); else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
else if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1); else if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1);
else if (strcmp(argv[1], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
else { else {
fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]); fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
return 1; return 1;