* samtools-0.1.2-10

[samtools.git] / glf.c

diff --git a/glf.c b/glf.c
index 302f9ef3bf06864ceba7b258ae3ccdd25f21c8be..0d09180c4befb49f4ff6f5129f8b58989e44808a 100644 (file)
--- a/glf.c
+++ b/glf.c
@@ -74,10 +74,10 @@ void glf_ref_write(glfFile fp, const char *str)
        bgzf_write(fp, str, n);
 }
 
-void glf_view_normal(const char *ref_name, glf2_t *g1)
+void glf_view_normal(const char *ref_name, glf3_t *g1, int pos)
 {
        int j;
-       printf("%s\t%d\t%c\t%d\t%d\t%d", ref_name, g1->pos + 1, "XACMGRSVTWYHKDBN"[g1->ref_base],
+       printf("%s\t%d\t%c\t%d\t%d\t%d", ref_name, pos + 1, "XACMGRSVTWYHKDBN"[g1->ref_base],
                   g1->depth, g1->max_mapQ, g1->min_lk);
        for (j = 0; j != 10; ++j) printf("\t%d", g1->lk[j]);
        printf("\n");
@@ -99,18 +99,20 @@ void glf_view(glfFile fp)
 {
        glf_header_t *h;
        char *name, *str;
-       glf2_t g2;
+       glf3_t g2;
        int max;
        
        h = glf_header_read(fp);
        str = 0; max = 0;
        while ((name = glf_ref_read(fp)) != 0) {
-               while (bgzf_read(fp, &g2, sizeof(glf2_t))) {
+               int pos = 0;
+               while (bgzf_read(fp, &g2, sizeof(glf3_t))) {
                        if (g2.type == GLF_TYPE_END) break;
-                       else if (g2.type == GLF_TYPE_NORMAL) glf_view_normal(name, &g2);
+                       pos += g2.offset;
+                       if (g2.type == GLF_TYPE_NORMAL) glf_view_normal(name, &g2, pos);
                        else if (g2.type == GLF_TYPE_INDEL) {
                                int16_t indel1, indel2;
-                               printf("%s\t%d\t*\t%d\t%d\t%d\t", name, g2.pos + 1, g2.depth, g2.max_mapQ, g2.min_lk);
+                               printf("%s\t%d\t*\t%d\t%d\t%d\t", name, pos + 1, g2.depth, g2.max_mapQ, g2.min_lk);
                                printf("%d\t%d\t%d\t", g2.lk[0], g2.lk[1], g2.lk[2]);
                                indel1 = *(int16_t*)(g2.lk + 3);
                                indel2 = *(int16_t*)(g2.lk + 5);