15 int cur_tid; //current tid;
16 float *wig_arr; // wiggle array
19 void generateWiggle(int tid) {
20 int chr_len = bam_in->header->target_len[tid];
21 char *chr_name = bam_in->header->target_name[tid];
25 for (int i = 0; i < chr_len; i++) {
32 fprintf(fo, "fixedStep chrom=%s start=%d step=1\n", chr_name, sp + 1);
33 for (int j = sp; j <= ep; j++) fprintf(fo, "%.7g\n", wig_arr[j]);
40 fprintf(fo, "fixedStep chrom=%s start=%d step=1\n", chr_name, sp + 1);
41 for (int j = sp; j <= ep; j++) fprintf(fo, "%.7g\n", wig_arr[j]);
45 int main(int argc, char* argv[]) {
49 printf("Usage : rsem-bam2wig sorted_bam_input wig_output wiggle_name\n");
53 bam_in = samopen(argv[1], "rb", NULL);
54 if (bam_in == 0) { fprintf(stderr, "Cannot open %s!\n", argv[1]); exit(-1); }
55 //assert(bam_in != 0);
58 fo = fopen(argv[2], "w");
59 fprintf(fo, "track type=wiggle_0 name=\"%s\" description=\"%s\" visibility=full\n", argv[3], argv[3]);
63 while (samread(bam_in, b) >= 0) {
64 if (b->core.tid != cur_tid) {
65 if (cur_tid >= 0) generateWiggle(cur_tid);
66 cur_tid = b->core.tid;
67 size_t len = sizeof(float) * bam_in->header->target_len[cur_tid];
68 wig_arr = (float*)realloc(wig_arr, len);
69 memset(wig_arr, 0, len);
72 float w = bam_aux2f(bam_aux_get(b, "ZW"));
73 int pos = b->core.pos;
74 uint32_t *p = bam1_cigar(b);
76 for (int i = 0; i < (int)b->core.n_cigar; i++, ++p) {
77 int op = *p & BAM_CIGAR_MASK;
78 int op_len = *p >> BAM_CIGAR_SHIFT;
81 //case BAM_CSOFT_CLIP : pos += op_len; break;
82 case BAM_CINS : pos += op_len; break;
84 for (int j = 0; j < op_len; j++, ++pos) wig_arr[pos] += w;
86 case BAM_CREF_SKIP : pos += op_len; break;
87 default : assert(false);
92 if (cnt % 1000000 == 0) printf("%d FIN\n", cnt);
94 if (cur_tid >= 0) generateWiggle(cur_tid);