# Uploaded samtools version 0.1.14-1.

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index eb69449f9e44d643ef43f31638fd8534c454c940..170bd843608b99aec35161141ee6afaad848db5e 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -82,7 +82,7 @@ static int usage(int is_long_help);
 
 int main_samview(int argc, char *argv[])
 {
-       int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, slx2sngr = 0, is_count = 0;
+       int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, slx2sngr = 0, is_count = 0;
        int of_type = BAM_OFDEC, is_long_help = 0;
        int count = 0;
        samfile_t *in = 0, *out = 0;
@@ -90,7 +90,7 @@ int main_samview(int argc, char *argv[])
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
-       while ((c = getopt(argc, argv, "Sbct:hHo:q:f:F:ul:r:xX?T:CR:")) >= 0) {
+       while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:CR:")) >= 0) {
                switch (c) {
                case 'c': is_count = 1; break;
                case 'C': slx2sngr = 1; break;
@@ -103,7 +103,8 @@ int main_samview(int argc, char *argv[])
                case 'f': g_flag_on = strtol(optarg, 0, 0); break;
                case 'F': g_flag_off = strtol(optarg, 0, 0); break;
                case 'q': g_min_mapQ = atoi(optarg); break;
-               case 'u': is_uncompressed = 1; break;
+               case 'u': compress_level = 0; break;
+               case '1': compress_level = 1; break;
                case 'l': g_library = strdup(optarg); break;
                case 'r': g_rg = strdup(optarg); break;
                case 'R': fn_rg = strdup(optarg); break;
@@ -114,7 +115,7 @@ int main_samview(int argc, char *argv[])
                default: return usage(is_long_help);
                }
        }
-       if (is_uncompressed) is_bamout = 1;
+       if (compress_level >= 0) is_bamout = 1;
        if (is_header_only) is_header = 1;
        if (is_bamout) strcat(out_mode, "b");
        else {
@@ -123,7 +124,11 @@ int main_samview(int argc, char *argv[])
        }
        if (is_bamin) strcat(in_mode, "b");
        if (is_header) strcat(out_mode, "h");
-       if (is_uncompressed) strcat(out_mode, "u");
+       if (compress_level >= 0) {
+               char tmp[2];
+               tmp[0] = compress_level + '0'; tmp[1] = '\0';
+               strcat(out_mode, tmp);
+       }
        if (argc == optind) return usage(is_long_help); // potential memory leak...
 
        // read the list of read groups
@@ -231,6 +236,7 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -H       print header only (no alignments)\n");
        fprintf(stderr, "         -S       input is SAM\n");
        fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");
+       fprintf(stderr, "         -1       fast compression (force -b)\n");
        fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
        fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");
        fprintf(stderr, "         -c       print only the count of matching records\n");