* Merge from branches/dev/

[samtools.git] / misc / maq2sam.c

diff --git a/misc/maq2sam.c b/misc/maq2sam.c
index e30aa925784198aab70132184a2dddb6f2e7705d..70ecf4145a73db6265b5df61cf18270b87d3f1c5 100644 (file)
--- a/misc/maq2sam.c
+++ b/misc/maq2sam.c
@@ -5,6 +5,8 @@
 #include <stdlib.h>
 #include <assert.h>
 
+#define PACKAGE_VERSION "0.1.1 (20090120)"
+
 //#define MAQ_LONGREADS
 
 #ifdef MAQ_LONGREADS
@@ -84,7 +86,7 @@ maqmap_t *maqmap_read_header(gzFile fp)
        return mm;
 }
 
-void maq2tam_core(gzFile fp)
+void maq2tam_core(gzFile fp, const char *rg)
 {
        maqmap_t *mm;
        maqmap1_t mm1, *m1;
@@ -141,6 +143,7 @@ void maq2tam_core(gzFile fp)
                for (j = 0; j != m1->size; ++j)
                        putchar((m1->seq[j]&0x3f) + 33);
                putchar('\t');
+               if (rg) printf("RG:Z:%s\t", rg);
                if (flag&4) {
                        printf("MF:i:%d\n", m1->flag);
                } else {
@@ -158,11 +161,12 @@ int main(int argc, char *argv[])
 {
        gzFile fp;
        if (argc == 1) {
-               fprintf(stderr, "Usage: maq2tam <in.map>\n");
+               fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
+               fprintf(stderr, "Usage: maq2sam <in.map> [<readGroup>]\n");
                return 1;
        }
        fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
-       maq2tam_core(fp);
+       maq2tam_core(fp, argc > 2? argv[2] : 0);
        gzclose(fp);
        return 0;
 }