Fix missing declaration for getopt on Mac OS X

[samtools.git] / padding.c

diff --git a/padding.c b/padding.c
index cf8ebfdce26b93bfefc2c794a49908c2fc61d48c..033a7916237f94314bcf9661880a3fcde4604156 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -57,7 +57,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
        bam_header_t *h;
        bam1_t *b;
        kstring_t r, q;
-        int r_tid = -1;
+       int r_tid = -1;
        uint32_t *cigar2 = 0;
        int n2 = 0, m2 = 0, *posmap = 0;
 
@@ -77,7 +77,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
                        r_tid = b->core.tid;
                        unpad_seq(b, &r);
                        if (h->target_len[r_tid] != r.l) {
-                               fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %i in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+                               fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
                                return -1;
                        }
                        write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));