* samtools-0.1.8-20 (r778)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 4bdc351e18a38322bd39dac30433aea3212b3b5a..cf98f69565ee6d52176df5ca5c9d14a44d2ef3e6 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -91,6 +91,21 @@ static khash_t(64) *load_pos(const char *fn, bam_header_t *h)
        return hash;
 }
 
+static inline int printw(int c, FILE *fp)
+{
+       char buf[16];
+       int l, x;
+       if (c == 0) return fputc('0', fp);
+       for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+       if (c < 0) buf[l++] = '-';
+       buf[l] = 0;
+       for (x = 0; x < l/2; ++x) {
+               int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
+       }
+       fputs(buf, fp);
+       return 0;
+}
+
 // an analogy to pileup_func() below
 static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
 {
@@ -162,7 +177,10 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
 
 static void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
 {
-       if (p->is_head) printf("^%c", p->b->core.qual > 93? 126 : p->b->core.qual + 33);
+       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)];
                rb = (ref && pos < ref_len)? ref[pos] : 'N';
@@ -170,19 +188,19 @@ static void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char
                else c = bam1_strand(p->b)? tolower(c) : toupper(c);
                putchar(c);
                if (p->indel > 0) {
-                       printf("+%d", p->indel);
+                       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) {
-                       printf("%d", p->indel);
+                       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('*');
+       } else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*');
        if (p->is_tail) putchar('$');
 }
 
@@ -256,12 +274,17 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                }
        }
        // print the first 3 columns
-       printf("%s\t%d\t%c\t", d->h->target_name[tid], pos + 1, rb);
+       fputs(d->h->target_name[tid], stdout); putchar('\t');
+       printw(pos+1, stdout); putchar('\t'); putchar(rb); putchar('\t');
        // print consensus information if required
-       if (d->format & BAM_PLF_CNS)
-               printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[cns>>28], cns>>8&0xff, cns&0xff, cns>>16&0xff);
+       if (d->format & BAM_PLF_CNS) {
+               putchar(bam_nt16_rev_table[cns>>28]); putchar('\t');
+               printw(cns>>8&0xff, stdout); putchar('\t');
+               printw(cns&0xff, stdout); putchar('\t');
+               printw(cns>>16&0xff, stdout); putchar('\t');
+       }
        // print pileup sequences
-       printf("%d\t", n);
+       printw(n, stdout); putchar('\t');
        rms_aux = 0; // we need to recalculate rms_mapq when -c is not flagged on the command line
        for (i = 0; i < n; ++i) {
                const bam_pileup1_t *p = pu + i;
@@ -310,7 +333,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                for (i = 0; i < n; ++i) {
                        int x = pu[i].qpos;
                        int l = pu[i].b->core.l_qseq;
-                       printf("%d,", x < l/2? x+1 : -((l-1)-x+1));
+                       printw(x < l/2? x+1 : -((l-1)-x+1), stdout); putchar(',');
                }
        }
        putchar('\n');