transcripts.buildMappings(in->header->n_targets, in->header->target_name);
bam_header_t *out_header = sam_header_read2(chr_list);
+
refmap.clear();
for (int i = 0; i < out_header->n_targets; i++) {
refmap[out_header->target_name[i]] = i;
}
- append_header_text(out_header, in->header->text, in->header->l_text);
+ if (in->header->l_text > 0) {
+ char comment[] = "@CO\tThis BAM file is processed by rsem-tbam2gam to convert from transcript coordinates into genomic coordinates.\n";
+ int comment_len = strlen(comment);
+
+ //Filter @SQ fields if the BAM file is user provided
+ char *text = in->header->text;
+ int l_text = in->header->l_text;
+ char *new_text = new char[l_text + comment_len];
+ int pos = 0, s = 0;
+ while (pos < l_text) {
+ if ((pos + 2 < l_text) && (text[pos] == '@') && (text[pos + 1] == 'S') && (text[pos + 2] == 'Q')) {
+ pos += 3;
+ while (pos < l_text && text[pos] != '\n') ++pos;
+ }
+ else new_text[s++] = text[pos];
+ ++pos;
+ }
+ strncpy(new_text + s, comment, comment_len);
+ s += comment_len;
+
+ append_header_text(out_header, new_text, s);
+ delete[] new_text;
+ }
out = samopen(outF, "wb", out_header);
assert(out != 0);
// at least one segment is not properly mapped
bool notgood = (b->core.flag & 0x0004) || (isPaired && (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 (isPaired && notgood) assert((b->core.flag & 0x0004) && (b2->core.flag & 0x0004));
+ 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;
+ }
+ }
+ const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);
- if (!notgood) {
- if (isPaired) assert((b->core.tid == b2->core.tid) && (b->core.flag & 0x0040) && (b2->core.flag & 0x0080)); // for collapsing
-
- const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);
-
- convert(b, transcript);
- if (isPaired) {
- convert(b2, transcript);
- b->core.mpos = b2->core.pos;
- b2->core.mpos = b->core.pos;
- }
-
- if (cqname != bam1_qname(b)) {
- writeCollapsedLines();
- cqname = bam1_qname(b);
- collapseMap.init(isPaired);
- }
- collapseMap.insert(b, b2, bam_aux2f(bam_aux_get(b, "ZW")));
+ convert(b, transcript);
+ if (isPaired) {
+ convert(b2, transcript);
+ b->core.mpos = b2->core.pos;
+ b2->core.mpos = b->core.pos;
+ }
+
+ if (cqname != bam1_qname(b)) {
+ writeCollapsedLines();
+ cqname = bam1_qname(b);
+ collapseMap.init(isPaired);
+ }
+
+ uint8_t *p = bam_aux_get(b, "ZW");
+ float prb = (p != NULL? bam_aux2f(p) : 1.0);
+ collapseMap.insert(b, b2, prb);
}
else {
- assert(cqname != bam1_qname(b));
+ assert(cqname != bam1_qname(b));
- writeCollapsedLines();
- cqname = bam1_qname(b);
- collapseMap.init(isPaired);
+ writeCollapsedLines();
+ cqname = bam1_qname(b);
+ collapseMap.init(isPaired);
- samwrite(out, b);
- if (isPaired) samwrite(out, b2);
+ samwrite(out, b);
+ if (isPaired) samwrite(out, b2);
}
-
}
writeCollapsedLines();
bam1_t *tmp_b = NULL,*tmp_b2 = NULL;
float prb;
bool isPaired;
+ uint8_t *p;
if (!collapseMap.empty(isPaired)) {
while (collapseMap.next(tmp_b, tmp_b2, prb)) {
- memcpy(bam_aux_get(tmp_b, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));
- tmp_b->core.qual = getMAPQ(prb);
+ p = bam_aux_get(tmp_b, "ZW");
+ if (p != NULL) {
+ memcpy(bam_aux_get(tmp_b, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));
+ tmp_b->core.qual = getMAPQ(prb);
+ }
+ // otherwise, just use the MAPQ score of the orignal alignment
+
samwrite(out, tmp_b);
if (isPaired) {
- memcpy(bam_aux_get(tmp_b2, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));
- tmp_b2->core.qual = tmp_b->core.qual;
- samwrite(out, tmp_b2);
+ if (p != NULL) memcpy(bam_aux_get(tmp_b2, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));
+ tmp_b2->core.qual = tmp_b->core.qual;
+ samwrite(out, tmp_b2);
}
bam_destroy1(tmp_b);
if (isPaired) bam_destroy1(tmp_b2);