diff bwa-0.6.2/bwtsw2_main.c @ 2:a294fbfcb1db draft default tip

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/bwtsw2_main.c	Fri Jul 18 07:55:59 2014 -0400
@@ -0,0 +1,95 @@
+#include <unistd.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <math.h>
+#include "bwt.h"
+#include "bwtsw2.h"
+#include "utils.h"
+
+int bwa_bwtsw2(int argc, char *argv[])
+{
+	extern char *bwa_infer_prefix(const char *hint);
+	bsw2opt_t *opt;
+	bwt_t *target;
+	char buf[1024], *prefix;
+	bntseq_t *bns;
+	int c;
+
+	opt = bsw2_init_opt();
+	srand48(11);
+	while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:MI:S")) >= 0) {
+		switch (c) {
+		case 'q': opt->q = atoi(optarg); break;
+		case 'r': opt->r = atoi(optarg); break;
+		case 'a': opt->a = atoi(optarg); break;
+		case 'b': opt->b = atoi(optarg); break;
+		case 'w': opt->bw = atoi(optarg); break;
+		case 'T': opt->t = atoi(optarg); break;
+		case 't': opt->n_threads = atoi(optarg); break;
+		case 'z': opt->z = atoi(optarg); break;
+		case 's': opt->is = atoi(optarg); break;
+		case 'm': opt->mask_level = atof(optarg); break;
+		case 'c': opt->coef = atof(optarg); break;
+		case 'N': opt->t_seeds = atoi(optarg); break;
+		case 'M': opt->multi_2nd = 1; break;
+		case 'H': opt->hard_clip = 1; break;
+		case 'f': xreopen(optarg, "w", stdout); break;
+		case 'I': opt->max_ins = atoi(optarg); break;
+		case 'S': opt->skip_sw = 1; break;
+		}
+	}
+	opt->qr = opt->q + opt->r;
+
+	if (optind + 2 > argc) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   bwa bwasw [options] <target.prefix> <query.fa> [query2.fa]\n\n");
+		fprintf(stderr, "Options: -a INT   score for a match [%d]\n", opt->a);
+		fprintf(stderr, "         -b INT   mismatch penalty [%d]\n", opt->b);
+		fprintf(stderr, "         -q INT   gap open penalty [%d]\n", opt->q);
+		fprintf(stderr, "         -r INT   gap extension penalty [%d]\n", opt->r);
+		fprintf(stderr, "         -w INT   band width [%d]\n", opt->bw);
+		fprintf(stderr, "         -m FLOAT mask level [%.2f]\n", opt->mask_level);
+		fprintf(stderr, "\n");
+		fprintf(stderr, "         -t INT   number of threads [%d]\n", opt->n_threads);
+		fprintf(stderr, "         -f FILE  file to output results to instead of stdout\n");
+		fprintf(stderr, "         -H       in SAM output, use hard clipping instead of soft clipping\n");
+		fprintf(stderr, "         -M       mark multi-part alignments as secondary\n");
+		fprintf(stderr, "         -S       skip Smith-Waterman read pairing\n");
+		fprintf(stderr, "         -I INT   ignore pairs with insert >=INT for inferring the size distr [%d]\n", opt->max_ins);
+		fprintf(stderr, "\n");
+		fprintf(stderr, "         -T INT   score threshold divided by a [%d]\n", opt->t);
+		fprintf(stderr, "         -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef);
+		fprintf(stderr, "         -z INT   Z-best [%d]\n", opt->z);
+		fprintf(stderr, "         -s INT   maximum seeding interval size [%d]\n", opt->is);
+		fprintf(stderr, "         -N INT   # seeds to trigger reverse alignment [%d]\n", opt->t_seeds);
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Note: For long Illumina, 454 and Sanger reads, assembly contigs, fosmids and\n");
+		fprintf(stderr, "      BACs, the default setting usually works well. For the current PacBio\n");
+		fprintf(stderr, "      reads (end of 2010), '-b5 -q2 -r1 -z10' is recommended. One may also\n");
+		fprintf(stderr, "      increase '-z' for better sensitivity.\n");
+		fprintf(stderr, "\n");
+
+		return 1;
+	}
+
+	// adjust opt for opt->a
+	opt->t *= opt->a;
+	opt->coef *= opt->a;
+
+	if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
+		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
+		return 0;
+	}
+	strcpy(buf, prefix); target = bwt_restore_bwt(strcat(buf, ".bwt"));
+	strcpy(buf, prefix); bwt_restore_sa(strcat(buf, ".sa"), target);
+	bns = bns_restore(prefix);
+
+	bsw2_aln(opt, bns, target, argv[optind+1], optind+2 < argc? argv[optind+2] : 0);
+
+	bns_destroy(bns);
+	bwt_destroy(target);
+	free(opt); free(prefix);
+	
+	return 0;
+}