improve pileup a little bit

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index cf98f69565ee6d52176df5ca5c9d14a44d2ef3e6..f0e63ce62cd91cc6cada955eaa19c9b2493e1872 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -175,32 +175,33 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
        return 0;
 }
 
-static void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
+static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
 {
+       int j;
        if (p->is_head) {
                putchar('^');
                putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33);
        }
        if (!p->is_del) {
-               int j, rb, c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+               int rb, c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
                rb = (ref && pos < ref_len)? ref[pos] : 'N';
                if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
                else c = bam1_strand(p->b)? tolower(c) : toupper(c);
                putchar(c);
-               if (p->indel > 0) {
-                       putchar('+'); printw(p->indel, stdout);
-                       for (j = 1; j <= p->indel; ++j) {
-                               c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
-                               putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
-                       }
-               } else if (p->indel < 0) {
-                       printw(p->indel, stdout);
-                       for (j = 1; j <= -p->indel; ++j) {
-                               c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
-                               putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
-                       }
-               }
        } else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*');
+       if (p->indel > 0) {
+               putchar('+'); printw(p->indel, stdout);
+               for (j = 1; j <= p->indel; ++j) {
+                       int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
+                       putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
+               }
+       } else if (p->indel < 0) {
+               printw(p->indel, stdout);
+               for (j = 1; j <= -p->indel; ++j) {
+                       int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
+                       putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
+               }
+       }
        if (p->is_tail) putchar('$');
 }