Update to the latest modfication 0.5.9rc1-2. Update ChangeLog

ChangeLog

@@ -1,3 +1,52 @@
+------------------------------------------------------------------------
+r1605 | lh3 | 2010-12-29 20:20:20 -0500 (Wed, 29 Dec 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.9rc1-2 (r1605)
+ * fixed a typo/bug in bwasw
+
+------------------------------------------------------------------------
+r1587 | lh3 | 2010-12-21 18:48:30 -0500 (Tue, 21 Dec 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+
+a typo in the manual
+
+------------------------------------------------------------------------
+r1586 | lh3 | 2010-12-21 18:47:48 -0500 (Tue, 21 Dec 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/utils.c
+   M /branches/prog/bwa/utils.h
+
+ * bwa-0.5.9rc1-1 (r1586)
+ * a few patches by John
+
+------------------------------------------------------------------------
+r1562 | lh3 | 2010-12-10 01:02:06 -0500 (Fri, 10 Dec 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+
+documentation on specifying @RG
+
+------------------------------------------------------------------------
+r1561 | lh3 | 2010-12-10 00:45:40 -0500 (Fri, 10 Dec 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.5.9rc1 (r1561)
+
 ------------------------------------------------------------------------
 r1560 | lh3 | 2010-12-10 00:29:08 -0500 (Fri, 10 Dec 2010) | 3 lines
 Changed paths:

bwa.1

@@ -40,7 +40,7 @@ each individual read, and the
 .B `samse/sampe'
 command, which converts SA coordinates to chromosomal coordinate and
 pairs reads (for `sampe'). The second algorithm is invoked by the
-.B `dbtwsw'
+.B `bwasw'
 command. It works for single-end reads only.
 
 .SH COMMANDS AND OPTIONS

bwape.c

@@ -45,6 +45,7 @@ int bwa_approx_mapQ(const bwa_seq_t *p, int mm);
 void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2);
 bntseq_t *bwa_open_nt(const char *prefix);
 void bwa_print_sam_SQ(const bntseq_t *bns);
+void bwa_print_sam_PG();
 
 pe_opt_t *bwa_init_pe_opt()
 {
@@ -689,6 +690,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 
 	// core loop
 	bwa_print_sam_SQ(bns);
+	bwa_print_sam_PG();
 	while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, opt.mode & BWA_MODE_COMPREAD, opt.trim_qual)) != 0) {
 		int cnt_chg;
 		isize_info_t ii;
@@ -763,7 +765,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
 		case 'n': popt->n_multi = atoi(optarg); break;
 		case 'N': popt->N_multi = atoi(optarg); break;
 		case 'c': popt->ap_prior = atof(optarg); break;
-        case 'f': freopen(optarg, "w", stdout); break;
+		case 'f': xreopen(optarg, "w", stdout); break;
 		case 'A': popt->force_isize = 1; break;
 		default: return 1;
 		}

bwase.c

@@ -14,6 +14,8 @@
 int g_log_n[256];
 char *bwa_rg_line, *bwa_rg_id;
 
+void bwa_print_sam_PG();
+
 void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
 {
 	int i, cnt, best;
@@ -604,6 +606,7 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
 	if (!(opt.mode & BWA_MODE_COMPREAD)) // in color space; initialize ntpac
 		ntbns = bwa_open_nt(prefix);
 	bwa_print_sam_SQ(bns);
+	bwa_print_sam_PG();
 	// set ks
 	ks = bwa_open_reads(opt.mode, fn_fa);
 	// core loop
@@ -662,7 +665,7 @@ int bwa_sai2sam_se(int argc, char *argv[])
 			}
 			break;
 		case 'n': n_occ = atoi(optarg); break;
-        case 'f': freopen(optarg, "w", stdout); break;
+		case 'f': xreopen(optarg, "w", stdout); break;
 		default: return 1;
 		}
 	}

bwtaln.c

@@ -268,7 +268,7 @@ int bwa_aln(int argc, char *argv[])
 		case 'q': opt->trim_qual = atoi(optarg); break;
 		case 'c': opt->mode &= ~BWA_MODE_COMPREAD; break;
 		case 'N': opt->mode |= BWA_MODE_NONSTOP; opt->max_top2 = 0x7fffffff; break;
-        case 'f': freopen(optarg, "wb", stdout); break;
+		case 'f': xreopen(optarg, "wb", stdout); break;
 		case 'b': opt->mode |= BWA_MODE_BAM; break;
 		case '0': opt->mode |= BWA_MODE_BAM_SE; break;
 		case '1': opt->mode |= BWA_MODE_BAM_READ1; break;

bwtsw2_aux.c

@@ -290,7 +290,7 @@ static void flag_fr(bwtsw2_t *b[2])
 	for (i = 0; i < b[0]->n; ++i) {
 		bsw2hit_t *p = b[0]->hits + i;
 		for (j = 0; j < b[1]->n; ++j) {
-			bsw2hit_t *q = b[1]->hits + i;
+			bsw2hit_t *q = b[1]->hits + j;
 			if (q->beg == p->beg && q->end == p->end && q->k == p->k && q->len == p->len && q->G == p->G) {
 				q->flag |= 0x30000; p->flag |= 0x30000;
 				break;

bwtsw2_main.c

@@ -5,6 +5,7 @@
 #include <math.h>
 #include "bwt.h"
 #include "bwtsw2.h"
+#include "utils.h"
 
 int bwa_bwtsw2(int argc, char *argv[])
 {
@@ -32,7 +33,7 @@ int bwa_bwtsw2(int argc, char *argv[])
 		case 'c': opt->coef = atof(optarg); break;
 		case 'N': opt->t_seeds = atoi(optarg); break;
 		case 'H': opt->hard_clip = 1; break;
-        case 'f': freopen(optarg, "w", stdout);
+		case 'f': xreopen(optarg, "w", stdout); break;
 		}
 	}
 	opt->qr = opt->q + opt->r;

main.c

@@ -3,7 +3,7 @@
 #include "main.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.5.9rc1 (r1561)"
+#define PACKAGE_VERSION "0.5.9rc1-2 (r1605)"
 #endif
 
 static int usage()
@@ -31,6 +31,11 @@ static int usage()
 	return 1;
 }
 
+void bwa_print_sam_PG()
+{
+	printf("@PG\tID:bwa\tPN:bwa\tVN:%s\n", PACKAGE_VERSION);
+}
+
 int main(int argc, char *argv[])
 {
 	if (argc < 2) return usage();

utils.c

@@ -43,6 +43,16 @@ FILE *err_xopen_core(const char *func, const char *fn, const char *mode)
 	}
 	return fp;
 }
+FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp)
+{
+	if (freopen(fn, mode, fp) == 0) {
+		fprintf(stderr, "[%s] fail to open file '%s': ", func, fn);
+		perror(NULL);
+		fprintf(stderr, "Abort!\n");
+		abort();
+	}
+	return fp;
+}
 gzFile err_xzopen_core(const char *func, const char *fn, const char *mode)
 {
 	gzFile fp;

utils.h

@@ -33,6 +33,7 @@
 
 #define err_fatal_simple(msg) err_fatal_simple_core(__func__, msg)
 #define xopen(fn, mode) err_xopen_core(__func__, fn, mode)
+#define xreopen(fn, mode, fp) err_xreopen_core(__func__, fn, mode, fp)
 #define xzopen(fn, mode) err_xzopen_core(__func__, fn, mode)
 #define xassert(cond, msg) if ((cond) == 0) err_fatal_simple_core(__func__, msg)
 
@@ -43,6 +44,7 @@ extern "C" {
 	void err_fatal(const char *header, const char *fmt, ...);
 	void err_fatal_simple_core(const char *func, const char *msg);
 	FILE *err_xopen_core(const char *func, const char *fn, const char *mode);
+	FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp);
 	gzFile err_xzopen_core(const char *func, const char *fn, const char *mode);
 
 #ifdef __cplusplus