1 #ifndef BAMCONVERTER_H_
2 #define BAMCONVERTER_H_
13 #include "sam_rsem_aux.h"
14 #include "sam_rsem_cvt.h"
18 #include "Transcript.h"
19 #include "Transcripts.h"
23 BamConverter(const char*, const char*, const char*, Transcripts&);
29 Transcripts& transcripts;
31 std::map<std::string, int> refmap;
32 std::map<std::string, int>::iterator iter;
34 CollapseMap collapseMap;
36 void convert(bam1_t*, const Transcript&);
38 void writeCollapsedLines();
39 void flipSeq(uint8_t*, int);
40 void flipQual(uint8_t*, int);
41 void addXSTag(bam1_t*, const Transcript&);
44 BamConverter::BamConverter(const char* inpF, const char* outF, const char* chr_list, Transcripts& transcripts)
45 : transcripts(transcripts)
47 if (transcripts.getType() != 0)
48 exitWithError("Genome information is not provided! RSEM cannot convert the transcript bam file!");
50 in = samopen(inpF, "rb", NULL);
53 bam_header_t *out_header = sam_header_read2(chr_list);
55 for (int i = 0; i < out_header->n_targets; i++) {
56 refmap[out_header->target_name[i]] = i;
59 append_header_text(out_header, in->header->text, in->header->l_text);
61 out = samopen(outF, "wb", out_header);
64 bam_header_destroy(out_header);
67 BamConverter::~BamConverter() {
72 void BamConverter::process() {
75 bool isPaired = false;
80 b = bam_init1(); b2 = bam_init1();
82 while (samread(in, b) >= 0) {
84 isPaired = (b->core.flag & 0x0001) > 0;
86 assert(samread(in, b2) >= 0 && (b2->core.flag & 0x0001) && b->core.tid == b2->core.tid);
87 assert((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)); // for collapsing
91 if (cnt % 1000000 == 0) { printf("."); fflush(stdout); }
93 // at least one segment is not properly mapped
94 if ((b->core.flag & 0x0004) || isPaired && (b2->core.flag & 0x0004)) continue;
96 const Transcript& transcript = transcripts.getTranscriptAt(b->core.tid + 1);
98 convert(b, transcript);
100 convert(b2, transcript);
101 b->core.mpos = b2->core.pos;
102 b2->core.mpos = b->core.pos;
105 if (cqname != bam1_qname(b)) {
106 writeCollapsedLines();
107 cqname = bam1_qname(b);
108 collapseMap.init(isPaired);
111 collapseMap.insert(b, b2, bam_aux2f(bam_aux_get(b, "ZW")));
114 writeCollapsedLines();
119 if (cnt >= 1000000) printf("\n");
122 void BamConverter::convert(bam1_t* b, const Transcript& transcript) {
123 int pos = b->core.pos;
124 int readlen = b->core.l_qseq;
126 if (readlen == 0) exitWithError("One alignment line has SEQ field as *. RSEM does not support this currently!");
128 iter = refmap.find(transcript.getSeqName());
129 assert(iter != refmap.end());
130 b->core.tid = iter->second;
131 if (b->core.flag & 0x0001) { b->core.mtid = b->core.tid; }
132 b->core.qual = 255; // set to not available temporarily
134 if (transcript.getStrand() == '-') {
135 b->core.flag ^= 0x0010;
136 if (b->core.flag & 0x0001) {
137 b->core.flag ^= 0x0020;
138 b->core.isize = -b->core.isize;
140 flipSeq(bam1_seq(b), readlen);
141 flipQual(bam1_qual(b), readlen);
144 std::vector<uint32_t> data;
147 int core_pos, core_n_cigar;
148 tr2chr(transcript, pos + 1, pos + readlen, core_pos, core_n_cigar, data);
149 assert(core_pos >= 0);
151 int rest_len = b->data_len - b->core.l_qname - b->core.n_cigar * 4;
152 b->data_len = b->core.l_qname + core_n_cigar * 4 + rest_len;
154 uint8_t* pt = b->data + b->core.l_qname;
155 memmove(pt + core_n_cigar * 4, pt + b->core.n_cigar * 4, rest_len);
156 for (int i = 0; i < core_n_cigar; i++) { memmove(pt, &data[i], 4); pt += 4; }
158 b->core.pos = core_pos;
159 b->core.n_cigar = core_n_cigar;
160 b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&(b->core), bam1_cigar(b)));
162 addXSTag(b, transcript); // check if need to add XS tag, if need, add it
165 inline void BamConverter::writeCollapsedLines() {
166 bam1_t *tmp_b = NULL,*tmp_b2 = NULL;
170 if (!collapseMap.empty(isPaired)) {
171 while (collapseMap.next(tmp_b, tmp_b2, prb)) {
172 memcpy(bam_aux_get(tmp_b, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));
173 tmp_b->core.qual = getMAPQ(prb);
174 if (tmp_b->core.qual > 0) {
175 samwrite(out, tmp_b);
177 memcpy(bam_aux_get(tmp_b2, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));
178 tmp_b2->core.qual = tmp_b->core.qual;
179 samwrite(out, tmp_b2);
183 if (isPaired) bam_destroy1(tmp_b2);
189 inline void BamConverter::flipSeq(uint8_t* s, int readlen) {
191 std::vector<uint8_t> seq;
195 for (int i = 0; i < readlen; i++) {
196 switch (bam1_seqi(s, readlen - i - 1)) {
197 case 1: base = 8; break;
198 case 2: base = 4; break;
199 case 4: base = 2; break;
200 case 8: base = 1; break;
201 case 15: base = 15; break;
202 default: assert(false);
204 code |= base << (4 * (1 - i % 2));
205 if (i % 2 == 1) { seq.push_back(code); code = 0; }
207 if (readlen % 2 == 1) { seq.push_back(code); }
209 for (int i = 0; i < (int)seq.size(); i++) s[i] = seq[i];
212 inline void BamConverter::flipQual(uint8_t* q, int readlen) {
213 int32_t mid = readlen / 2;
215 for (int i = 0; i < mid; i++) {
216 tmp = q[i]; q[i] = q[readlen - i - 1]; q[readlen -i -1] = tmp;
220 inline void BamConverter::addXSTag(bam1_t* b, const Transcript& transcript) {
221 uint32_t* p = bam1_cigar(b);
223 for (int i = 0; i < (int)b->core.n_cigar; i++)
224 if ((*(p + i) & BAM_CIGAR_MASK) == BAM_CREF_SKIP) { hasN = true; break; }
226 char strand = transcript.getStrand();
227 bam_aux_append(b, "XS", 'A', 1, (uint8_t*)&strand);
230 #endif /* BAMCONVERTER_H_ */