main.c don't print mismatch

src/Makefile

@@ -1,6 +1,6 @@
 CC = gcc
 CXX = g++
-CFLAGS := -Wall -pipe -g#-O3
+CFLAGS := -Wall -pipe -O3
 CXXFLAGS := $(CFLAGS)
 LOBJS = ssw.o
 LCPPOBJS = ssw_cpp.o

src/main.c

@@ -1,7 +1,7 @@
 /*  main.c
  *  Created by Mengyao Zhao on 06/23/11.
  *	Version 1.0
- *  Last revision by Mengyao Zhao on 06/24/16.
+ *  Last revision by Mengyao Zhao on 07/19/16.
  */
 
 #include <stdlib.h>
@@ -168,7 +168,7 @@ static void ssw_write (s_align* a,
 				uint32_t length = cigar_int_to_len(a->cigar[c]);
 				fprintf(stdout, "%lu%c", (unsigned long)length, letter);
 			}
-			fprintf(stderr, "%s\tmismatch: %d\n", read->name.s, mismatch);
+	//		fprintf(stderr, "%s\tmismatch: %d\n", read->name.s, mismatch);
 			fprintf(stdout, "\t*\t0\t0\t");
 			for (c = a->read_begin1; c <= a->read_end1; ++c) fprintf(stdout, "%c", read_seq[c]);
 			fprintf(stdout, "\t");

src/ssw.c

@@ -857,17 +857,12 @@ void align_destroy (s_align* a) {
 }
 
 uint32_t* add_cigar (uint32_t* new_cigar, int32_t* p, int32_t* s, uint32_t length, char op) {
-//	int i;
 	if ((*p) >= (*s)) {
-//		fprintf(stderr, "s_old:%d\tp: %d\n", *s, *p);
-//		for (i = 0; i < *s; ++i) fprintf(stderr, "new_cigar[%d]: %d\n", i, new_cigar[i]);
 		++(*s);
 		kroundup32(*s);
-//		fprintf(stderr, "s: %d\tnew_cigar_before: %p\n", *s, new_cigar);
 		new_cigar = (uint32_t*)realloc(new_cigar, (*s)*sizeof(uint32_t));
 	}
 	new_cigar[(*p) ++] = to_cigar_int(length, op);
-//	fprintf(stderr, "new_cigar_after: %p\n", new_cigar);
 	return new_cigar;
 }
 
@@ -879,11 +874,9 @@ uint32_t* store_previous_m (int8_t choice,	// 0: current not M, 1: current match
 					   uint32_t* new_cigar) {
 
 	if ((*length_m) && (choice == 2 || !choice)) {
-//		fprintf(stderr, "call add_cigar in =\n");
 		new_cigar = add_cigar (new_cigar, p, s, (*length_m), '='); 
 		(*length_m) = 0;
 	} else if ((*length_x) && (choice == 1 || !choice)) { 
-//		fprintf(stderr, "call add_cigar in X\n");
 		new_cigar = add_cigar (new_cigar, p, s, (*length_x), 'X'); 
 		(*length_x) = 0;
 	}
@@ -936,20 +929,17 @@ int32_t mark_mismatch (int32_t ref_begin1,
 			read += length;
 			mismatch_length += length;
 			new_cigar = store_previous_m (0, &length_m, &length_x, &p, &s, new_cigar);			
-//		fprintf(stderr, "call add_cigar in I\n");
 			new_cigar = add_cigar (new_cigar, &p, &s, length, 'I'); 
 		}else if (op == 'D') {
 			ref += length;
 			mismatch_length += length;
 			new_cigar = store_previous_m (0, &length_m, &length_x, &p, &s, new_cigar);			
-//		fprintf(stderr, "call add_cigar in D\n");
 			new_cigar = add_cigar (new_cigar, &p, &s, length, 'D'); 
 		}
 	}
 	new_cigar = store_previous_m (0, &length_m, &length_x, &p, &s, new_cigar);
 
 	length = readLen - read_end1 - 1;
-//		fprintf(stderr, "call add_cigar in S\n");
 	if (length > 0) new_cigar = add_cigar(new_cigar, &p, &s, length, 'S');
 
 	(*cigarLen) = p;