bamcheck: new stats, number of filtered vs raw sequences

[samtools.git] / razip.c

diff --git a/razip.c b/razip.c
index 0b67c6c50cf62f4ccb12948fdf96dbc813633b87..825e73268114736530e35415f19f47af23dac03e 100644 (file)
--- a/razip.c
+++ b/razip.c
@@ -2,6 +2,8 @@
 #include <fcntl.h>
 #include <unistd.h>
 #include <errno.h>
+#include <stdlib.h>
+#include <string.h>
 #include "razf.h"
 
 #define WINDOW_SIZE 4096
@@ -25,7 +27,7 @@ static int write_open(const char *fn, int is_forced)
        int fd = -1;
        char c;
        if (!is_forced) {
-               if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0644)) < 0 && errno == EEXIST) {
+               if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
                        printf("razip: %s already exists; do you wish to overwrite (y or n)? ", fn);
                        scanf("%c", &c);
                        if (c != 'Y' && c != 'y') {
@@ -35,7 +37,7 @@ static int write_open(const char *fn, int is_forced)
                }
        }
        if (fd < 0) {
-               if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0644)) < 0) {
+               if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
                        fprintf(stderr, "razip: %s: Fail to write\n", fn);
                        exit(1);
                }
@@ -92,7 +94,7 @@ int main(int argc, char **argv)
                buffer = malloc(WINDOW_SIZE);
                while((c = read(f_src, buffer, WINDOW_SIZE)) > 0) razf_write(rz, buffer, c);
                razf_close(rz); // f_dst will be closed here
-               if (argc > optind) unlink(argv[optind]);
+               if (argc > optind && !pstdout) unlink(argv[optind]);
                free(buffer);
                close(f_src);
                return 0;