From 14aa43cca0116ba4dba6fa54d17d868c9ed5d13a Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 12 Feb 2014 15:39:02 -0500 Subject: [PATCH] r434: added the missing bwasw/aln commands! --- main.c | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/main.c b/main.c index f872917..86de68e 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.6a-r433" +#define PACKAGE_VERSION "0.7.6a-dev-r434" #endif 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 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_mem(int argc, char *argv[]); +int main_pemerge(int argc, char *argv[]); + char *bwa_pg; static int usage() @@ -29,6 +37,11 @@ static int usage() fprintf(stderr, "Command: index index sequences in the FASTA format\n"); fprintf(stderr, " mem BWA-MEM algorithm\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, " fa2pac convert FASTA to PAC format\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], "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], "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], "mem") == 0) ret = main_mem(argc-1, argv+1); + else if (strcmp(argv[1], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1); else { fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]); return 1;