144 lines
6.6 KiB
C
144 lines
6.6 KiB
C
/* The MIT License
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Copyright (c) 2018- Dana-Farber Cancer Institute
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2009-2018 Broad Institute, Inc.
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2008-2009 Genome Research Ltd. (GRL)
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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*/
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#include <stdio.h>
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#include <string.h>
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#include "kstring.h"
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#include "utils.h"
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#ifndef PACKAGE_VERSION
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#define PACKAGE_VERSION "v1.0-0.7.17"
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#endif
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int bwa_fa2pac(int argc, char *argv[]);
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int bwa_pac2bwt(int argc, char *argv[]);
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int bwa_bwtupdate(int argc, char *argv[]);
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int bwa_bwt2sa(int argc, char *argv[]);
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int bwa_bwt2bytesa(int argc, char *argv[]);
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int bwa_bwt2fmt(int argc, char *argv[]);
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int bwa_build_kmer(int argc, char *argv[]);
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int bwa_bwt2ert(int argc, char *argv[]);
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int bwa_index(int argc, char *argv[]);
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int bwt_bwtgen_main(int argc, char *argv[]);
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int bwa_aln(int argc, char *argv[]);
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int bwa_sai2sam_se(int argc, char *argv[]);
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int bwa_sai2sam_pe(int argc, char *argv[]);
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int bwa_bwtsw2(int argc, char *argv[]);
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int main_fastmap(int argc, char *argv[]);
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int main_mem(int argc, char *argv[]);
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int main_shm(int argc, char *argv[]);
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int main_pemerge(int argc, char *argv[]);
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int main_maxk(int argc, char *argv[]);
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static int usage()
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{
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fprintf(stderr, "\n");
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fprintf(stderr, "Program: fast-bwa-mem (alignment via Burrows-Wheeler transformation)\n");
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fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
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fprintf(stderr, "Contact: Heng Li <hli@ds.dfci.harvard.edu> (for bwa)\n\n");
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fprintf(stderr, "Contact: Zhonghai Zhang <zhangzhonghai@ict.ac.cn> (for fast-bwa-mem)\n\n");
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fprintf(stderr, "Usage: fastbwa <command> [options]\n\n");
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fprintf(stderr, "Command: index index sequences in the FASTA format\n");
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fprintf(stderr, " mem BWA-MEM algorithm\n");
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fprintf(stderr, " fastmap identify super-maximal exact matches\n");
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fprintf(stderr, " pemerge merge overlapping paired ends (EXPERIMENTAL)\n");
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fprintf(stderr, " aln gapped/ungapped alignment\n");
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fprintf(stderr, " samse generate alignment (single ended)\n");
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fprintf(stderr, " sampe generate alignment (paired ended)\n");
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fprintf(stderr, " bwasw BWA-SW for long queries (DEPRECATED)\n");
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fprintf(stderr, "\n");
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fprintf(stderr, " shm manage indices in shared memory\n");
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fprintf(stderr, " fa2pac convert FASTA to PAC format\n");
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fprintf(stderr, " pac2bwt generate BWT from PAC\n");
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fprintf(stderr, " pac2bwtgen alternative algorithm for generating BWT\n");
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fprintf(stderr, " bwtupdate update .bwt to the new format\n");
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fprintf(stderr, " bwt2sa generate SA from BWT and Occ\n");
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fprintf(stderr, " bwt2bytesa generate SA(using byte array) from BWT and Occ\n");
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fprintf(stderr, " bwt2fmt generate FMT-Index from BWT\n");
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fprintf(stderr, " buildkmer generate kmer index from FMT\n");
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fprintf(stderr, " bwt2ert generate ert index from BWT\n");
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fprintf(stderr, "\n");
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fprintf(stderr,
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"Note: To use BWA, you need to first index the genome with `bwa index'.\n"
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" There are three alignment algorithms in BWA: `mem', `bwasw', and\n"
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" `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'\n"
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" first. Please `man ./bwa.1' for the manual.\n\n");
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return 1;
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}
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int main(int argc, char *argv[])
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{
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extern char *bwa_pg;
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int i, ret;
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double t_real;
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kstring_t pg = {0,0,0};
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t_real = realtime();
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ksprintf(&pg, "@PG\tID:bwa\tPN:bwa\tVN:%s\tCL:%s", PACKAGE_VERSION, argv[0]);
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for (i = 1; i < argc; ++i) ksprintf(&pg, " %s", argv[i]);
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bwa_pg = pg.s;
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if (argc < 2) return usage();
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if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1);
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else if (strcmp(argv[1], "pac2bwt") == 0) ret = bwa_pac2bwt(argc-1, argv+1);
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else if (strcmp(argv[1], "pac2bwtgen") == 0) ret = bwt_bwtgen_main(argc-1, argv+1);
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else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1);
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else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1);
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else if (strcmp(argv[1], "bwt2bytesa") == 0) ret = bwa_bwt2bytesa(argc-1, argv+1);
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else if (strcmp(argv[1], "bwt2fmt") == 0) ret = bwa_bwt2fmt(argc-1, argv+1);
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else if (strcmp(argv[1], "buildkmer") == 0) ret = bwa_build_kmer(argc - 1, argv + 1);
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else if (strcmp(argv[1], "bwt2ert") == 0) ret = bwa_bwt2ert(argc-1, argv+1);
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else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1);
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else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1);
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else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1);
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else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1);
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else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
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else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
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else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
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else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
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else if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1);
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else if (strcmp(argv[1], "shm") == 0) ret = main_shm(argc-1, argv+1);
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else if (strcmp(argv[1], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
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else if (strcmp(argv[1], "maxk") == 0) ret = main_maxk(argc-1, argv+1);
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else {
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fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
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return 1;
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}
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err_fflush(stdout);
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err_fclose(stdout);
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if (ret == 0) {
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fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION);
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fprintf(stderr, "[%s] CMD:", __func__);
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for (i = 0; i < argc; ++i)
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fprintf(stderr, " %s", argv[i]);
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fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
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}
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free(bwa_pg);
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return ret;
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}
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