13 void add_bam_record_to_wiggle(const bam1_t *b, Wiggle& wiggle) {
14 uint8_t *p_tag = bam_aux_get(b, "ZW");
15 float w = (p_tag != NULL ? bam_aux2f(p_tag) : 1.0);
16 int pos = b->core.pos;
17 uint32_t *p = bam1_cigar(b);
19 for (int i = 0; i < (int)b->core.n_cigar; i++, ++p) {
20 int op = *p & BAM_CIGAR_MASK;
21 int op_len = *p >> BAM_CIGAR_SHIFT;
24 //case BAM_CSOFT_CLIP : pos += op_len; break;
25 case BAM_CINS : pos += op_len; break;
27 for (int j = 0; j < op_len; j++, ++pos) {
28 wiggle.read_depth[pos] += w;
31 case BAM_CREF_SKIP : pos += op_len; break;
32 default : assert(false);
37 void build_wiggles(const std::string& bam_filename,
38 WiggleProcessor& processor) {
39 samfile_t *bam_in = samopen(bam_filename.c_str(), "rb", NULL);
40 if (bam_in == 0) { fprintf(stderr, "Cannot open %s!\n", bam_filename.c_str()); exit(-1); }
42 bam_header_t *header = bam_in->header;
43 bool *used = new bool[header->n_targets];
44 memset(used, 0, sizeof(bool) * header->n_targets);
46 int cur_tid = -1; //current tid;
48 bam1_t *b = bam_init1();
50 while (samread(bam_in, b) >= 0) {
51 if (b->core.flag & 0x0004) continue;
53 if (b->core.tid != cur_tid) {
54 if (cur_tid >= 0) { used[cur_tid] = true; processor.process(wiggle); }
55 cur_tid = b->core.tid;
56 wiggle.name = header->target_name[cur_tid];
57 wiggle.length = header->target_len[cur_tid];
58 wiggle.read_depth.assign(wiggle.length, 0.0);
60 add_bam_record_to_wiggle(b, wiggle);
62 if (cnt % 1000000 == 0) std::cout<< cnt<< std::endl;
64 if (cur_tid >= 0) { used[cur_tid] = true; processor.process(wiggle); }
66 for (int32_t i = 0; i < header->n_targets; i++)
68 wiggle.name = header->target_name[i];
69 wiggle.length = header->target_len[i];
70 wiggle.read_depth.clear();
71 processor.process(wiggle);
79 UCSCWiggleTrackWriter::UCSCWiggleTrackWriter(const std::string& output_filename,
80 const std::string& track_name) {
81 fo = fopen(output_filename.c_str(), "w");
82 fprintf(fo, "track type=wiggle_0 name=\"%s\" description=\"%s\" visibility=full\n",
87 UCSCWiggleTrackWriter::~UCSCWiggleTrackWriter() {
91 void UCSCWiggleTrackWriter::process(const Wiggle& wiggle) {
94 if (wiggle.read_depth.empty()) return;
97 for (size_t i = 0; i < wiggle.length; i++) {
98 if (wiggle.read_depth[i] > 0) {
104 fprintf(fo, "fixedStep chrom=%s start=%d step=1\n", wiggle.name.c_str(), sp + 1);
105 for (int j = sp; j <= ep; j++) fprintf(fo, "%.7g\n", wiggle.read_depth[j]);
112 fprintf(fo, "fixedStep chrom=%s start=%d step=1\n", wiggle.name.c_str(), sp + 1);
113 for (int j = sp; j <= ep; j++) fprintf(fo, "%.7g\n", wiggle.read_depth[j]);
117 ReadDepthWriter::ReadDepthWriter(std::ostream& stream)
121 void ReadDepthWriter::process(const Wiggle& wiggle) {
123 stream_ << wiggle.name << '\t'
124 << wiggle.length << '\t';
126 if (wiggle.read_depth.empty()) { stream_ << "NA\n"; return; }
128 for (size_t i = 0; i < wiggle.length; ++i) {
129 if (i > 0) stream_ << ' ';
130 stream_ << wiggle.read_depth[i];