void writeCollapsedLines();
void flipSeq(uint8_t*, int);
void flipQual(uint8_t*, int);
- void addXSTag(bam1_t*, const Transcript&);
+ void modifyTags(bam1_t*, const Transcript&); // modify MD tag and XS tag if needed
};
BamConverter::BamConverter(const char* inpF, const char* outF, const char* chr_list, Transcripts& transcripts)
// at least one segment is not properly mapped
bool notgood = (b->core.flag & 0x0004) || (isPaired && (b2->core.flag & 0x0004));
-
- if (isPaired && notgood) assert((b->core.flag & 0x0004) && (b2->core.flag & 0x0004));
-
+ if (isPaired && notgood) general_assert((b->core.flag & 0x0004) && (b2->core.flag & 0x0004), cstrtos(bam1_qname(b)) + "'s two mates are not all marked as unalignable!");
if (!notgood) {
// for collapsing
if (isPaired) {
assert(b->core.tid == b2->core.tid);
+ general_assert(b->core.tid == b2->core.tid, cstrtos(bam1_qname(b)) + "'s two mates are aligned to two different transcripts!");
if ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)) {
bam1_t *tmp = b; b = b2; b2 = tmp;
}
b->core.n_cigar = core_n_cigar;
b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&(b->core), bam1_cigar(b)));
- addXSTag(b, transcript); // check if need to add XS tag, if need, add it
+ modifyTags(b, transcript); // check if need to add XS tag, if need, add it
}
inline void BamConverter::writeCollapsedLines() {
memcpy(bam_aux_get(tmp_b, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));
tmp_b->core.qual = getMAPQ(prb);
}
- else tmp_b->core.qual = getMAPQ(1.0);
+ // otherwise, just use the MAPQ score of the orignal alignment
+
samwrite(out, tmp_b);
if (isPaired) {
if (p != NULL) memcpy(bam_aux_get(tmp_b2, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));
}
}
-inline void BamConverter::addXSTag(bam1_t* b, const Transcript& transcript) {
- uint32_t* p = bam1_cigar(b);
+inline void BamConverter::modifyTags(bam1_t* b, const Transcript& transcript) {
+ char strand = transcript.getStrand();
+ uint8_t *s = NULL;
+
+ if (strand == '-') {
+ s = bam_aux_get(b, "MD");
+ if ((s != NULL) && (*(s) == 'Z') && (bam_aux2Z(s) != NULL)) {
+ char *mis = bam_aux2Z(s);
+ int len = strlen(mis);
+ char *tmp = new char[len];
+ int cur_type = -1, fr = -1, type, base;
+ for (int i = 0; i < len; i++) {
+ type = (mis[i] >= '0' && mis[i] <= '9');
+ if (cur_type != type) {
+ switch(cur_type) {
+ case 0:
+ base = len - 1;
+ if (mis[fr] == '^') { tmp[len - i] = mis[fr]; ++fr; ++base; }
+ for (int j = fr; j < i; j++) tmp[base - j] = ((mis[j] == 'A' || mis[j] == 'C' || mis[j] == 'G' || mis[j] == 'T') ? getOpp(mis[j]) : mis[j]);
+ break;
+ case 1:
+ base = len - i - fr;
+ for (int j = fr; j < i; j++) tmp[base + j] = mis[j];
+ break;
+ }
+ cur_type = type;
+ fr = i;
+ }
+ }
+ switch(cur_type) {
+ case 0:
+ base = len - 1;
+ if (mis[fr] == '^') { tmp[0] = mis[fr]; ++fr; ++base; }
+ for (int j = fr; j < len; j++) tmp[base - j] = ((mis[j] == 'A' || mis[j] == 'C' || mis[j] == 'G' || mis[j] == 'T') ? getOpp(mis[j]) : mis[j]);
+ break;
+ case 1:
+ for (int j = fr; j < len; j++) tmp[j - fr] = mis[j];
+ break;
+ }
+ strncpy(mis, tmp, len);
+ delete[] tmp;
+ }
+ }
+
+ // append XS:A field if necessary
+ s = bam_aux_get(b, "XS");
+ if (s != NULL) bam_aux_del(b, s);
bool hasN = false;
+ uint32_t* p = bam1_cigar(b);
for (int i = 0; i < (int)b->core.n_cigar; i++)
if ((*(p + i) & BAM_CIGAR_MASK) == BAM_CREF_SKIP) { hasN = true; break; }
- if (!hasN) return;
- char strand = transcript.getStrand();
- bam_aux_append(b, "XS", 'A', 1, (uint8_t*)&strand);
+ if (hasN) bam_aux_append(b, "XS", 'A', 1, (uint8_t*)&strand);
}
#endif /* BAMCONVERTER_H_ */