debug flag to measure memory

bwa.c

@@ -40,6 +40,7 @@
 #endif
 
 int bwa_verbose = 3;
+int bwa_dbg = 0;
 char bwa_rg_id[256];
 char *bwa_pg;
 

bwa.h

@@ -43,6 +43,8 @@
 #define BWTALGO_BWTSW 2
 #define BWTALGO_IS    3
 
+#define BWA_DBG_QNAME 0x1
+
 typedef struct {
 	bwt_t    *bwt; // FM-index
 	bntseq_t *bns; // information on the reference sequences
@@ -58,7 +60,7 @@ typedef struct {
 	char *name, *comment, *seq, *qual, *sam;
 } bseq1_t;
 
-extern int bwa_verbose;
+extern int bwa_verbose, bwa_dbg;
 extern char bwa_rg_id[256];
 
 #ifdef __cplusplus

bwamem.c

@@ -1223,10 +1223,12 @@ static void worker2(void *data, int i, int tid)
 		mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a, w->n_processed + i);
 		if (w->opt->flag & MEM_F_PRIMARY5) mem_reorder_primary5(w->opt->T, &w->regs[i]);
 		mem_reg2sam(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
+		fprintf(stderr, "Q\t%s\t%.3f\n", w->seqs[i].name, peakrss() / 1073741824.0);
 		free(w->regs[i].a);
 	} else {
 		if (bwa_verbose >= 4) printf("=====> Finalizing read pair '%s' <=====\n", w->seqs[i<<1|0].name);
 		mem_sam_pe(w->opt, w->bns, w->pac, w->pes, (w->n_processed>>1) + i, &w->seqs[i<<1], &w->regs[i<<1]);
+		fprintf(stderr, "Q\t%s\t%.3f\n", w->seqs[i<<1|0].name, peakrss() / 1073741824.0);
 		free(w->regs[i<<1|0].a); free(w->regs[i<<1|1].a);
 	}
 }

fastmap.c

@@ -156,7 +156,7 @@ int main_mem(int argc, char *argv[])
 
 	aux.opt = opt = mem_opt_init();
 	memset(&opt0, 0, sizeof(mem_opt_t));
-	while ((c = getopt(argc, argv, "51qpaMCSPVYjuk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
+	while ((c = getopt(argc, argv, "51qpaMCSPVYjuk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:F:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
 		else if (c == '1') no_mt_io = 1;
 		else if (c == 'x') mode = optarg;
@@ -192,6 +192,7 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'C') aux.copy_comment = 1;
 		else if (c == 'K') fixed_chunk_size = atoi(optarg);
 		else if (c == 'X') opt->mask_level = atof(optarg);
+		else if (c == 'F') bwa_dbg = atoi(optarg);
 		else if (c == 'h') {
 			opt0.max_XA_hits = opt0.max_XA_hits_alt = 1;
 			opt->max_XA_hits = opt->max_XA_hits_alt = strtol(optarg, &p, 10);

utils.c

@@ -279,17 +279,28 @@ int err_gzclose(gzFile file)
  * Timer *
  *********/
 
-double cputime()
+double cputime(void)
 {
 	struct rusage r;
 	getrusage(RUSAGE_SELF, &r);
 	return r.ru_utime.tv_sec + r.ru_stime.tv_sec + 1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec);
 }
 
-double realtime()
+double realtime(void)
 {
 	struct timeval tp;
 	struct timezone tzp;
 	gettimeofday(&tp, &tzp);
 	return tp.tv_sec + tp.tv_usec * 1e-6;
 }
+
+long peakrss(void)
+{
+	struct rusage r;
+	getrusage(RUSAGE_SELF, &r);
+#ifdef __linux__
+	return r.ru_maxrss * 1024;
+#else
+	return r.ru_maxrss;
+#endif
+}

utils.h

@@ -84,8 +84,9 @@ extern "C" {
 	int err_fclose(FILE *stream);
 	int err_gzclose(gzFile file);
 
-	double cputime();
-	double realtime();
+	double cputime(void);
+	double realtime(void);
+	long peakrss(void);
 
 	void ks_introsort_64 (size_t n, uint64_t *a);
 	void ks_introsort_128(size_t n, pair64_t *a);