// currently, this function ONLY works if each read has one hit
void bam_mating_core(bamFile in, bamFile out)
{
bam_header_t *header;
bam1_t *b[2];
int curr, has_prev, pre_end = 0, cur_end;
kstring_t str;
str.l = str.m = 0; str.s = 0;
header = bam_header_read(in);
bam_header_write(out, header);
b[0] = bam_init1();
b[1] = bam_init1();
curr = 0; has_prev = 0;
while (bam_read1(in, b[curr]) >= 0) {
bam1_t *cur = b[curr], *pre = b[1-curr];
if (cur->core.tid < 0) continue;
cur_end = bam_calend(&cur->core, bam1_cigar(cur));
if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP;
if (cur->core.flag & BAM_FSECONDARY) continue; // skip secondary alignments
if (has_prev) {
if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
&& !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // set TLEN/ISIZE
{
uint32_t cur5, pre5;
cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : pre->core.pos;
cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
} else cur->core.isize = pre->core.isize = 0;
if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
else cur->core.flag &= ~BAM_FMREVERSE;
if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
else pre->core.flag &= ~BAM_FMREVERSE;
if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
bam_template_cigar(pre, cur, &str);
bam_write1(out, pre);
bam_write1(out, cur);
has_prev = 0;
} else { // unpaired or singleton
pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
if (pre->core.flag & BAM_FPAIRED) {
pre->core.flag |= BAM_FMUNMAP;
pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
}
bam_write1(out, pre);
}
} else has_prev = 1;
curr = 1 - curr;
pre_end = cur_end;
}
if (has_prev) bam_write1(out, b[1-curr]);
bam_header_destroy(header);
bam_destroy1(b[0]);
bam_destroy1(b[1]);
free(str.s);
}
// currently, this function ONLY works if each read has one hit
static void bam_mating_core(samFile* in, samFile* out, int remove_reads, int proper_pair_check, int add_ct)
{
bam_hdr_t *header;
bam1_t *b[2];
int curr, has_prev, pre_end = 0, cur_end = 0;
kstring_t str;
str.l = str.m = 0; str.s = 0;
header = sam_hdr_read(in);
if (header == NULL) {
fprintf(stderr, "[bam_mating_core] ERROR: Couldn't read header\n");
exit(1);
}
// Accept unknown, unsorted, or queryname sort order, but error on coordinate sorted.
if ((header->l_text > 3) && (strncmp(header->text, "@HD", 3) == 0)) {
char *p, *q;
p = strstr(header->text, "\tSO:coordinate");
q = strchr(header->text, '\n');
// Looking for SO:coordinate within the @HD line only
// (e.g. must ignore in a @CO comment line later in header)
if ((p != 0) && (p < q)) {
fprintf(stderr, "[bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.\n");
exit(1);
}
}
sam_hdr_write(out, header);
b[0] = bam_init1();
b[1] = bam_init1();
curr = 0; has_prev = 0;
while (sam_read1(in, header, b[curr]) >= 0) {
bam1_t *cur = b[curr], *pre = b[1-curr];
if (cur->core.flag & BAM_FSECONDARY)
{
if ( !remove_reads ) sam_write1(out, header, cur);
continue; // skip secondary alignments
}
if (cur->core.flag & BAM_FSUPPLEMENTARY)
{
sam_write1(out, header, cur);
continue; // pass supplementary alignments through unchanged (TODO:make them match read they came from)
}
if (cur->core.tid < 0 || cur->core.pos < 0) // If unmapped set the flag
{
cur->core.flag |= BAM_FUNMAP;
}
if ((cur->core.flag&BAM_FUNMAP) == 0) // If mapped calculate end
{
cur_end = bam_endpos(cur);
// Check cur_end isn't past the end of the contig we're on, if it is set the UNMAP'd flag
if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP;
}
if (has_prev) { // do we have a pair of reads to examine?
if (strcmp(bam_get_qname(cur), bam_get_qname(pre)) == 0) { // identical pair name
pre->core.flag |= BAM_FPAIRED;
cur->core.flag |= BAM_FPAIRED;
sync_mate(pre, cur);
if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
&& !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // if safe set TLEN/ISIZE
{
uint32_t cur5, pre5;
cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : pre->core.pos;
cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
} else cur->core.isize = pre->core.isize = 0;
if (add_ct) bam_template_cigar(pre, cur, &str);
// TODO: Add code to properly check if read is in a proper pair based on ISIZE distribution
if (proper_pair_check && !plausibly_properly_paired(pre,cur)) {
pre->core.flag &= ~BAM_FPROPER_PAIR;
cur->core.flag &= ~BAM_FPROPER_PAIR;
}
// Write out result
if ( !remove_reads ) {
sam_write1(out, header, pre);
sam_write1(out, header, cur);
} else {
// If we have to remove reads make sure we do it in a way that doesn't create orphans with bad flags
if(pre->core.flag&BAM_FUNMAP) cur->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
if(cur->core.flag&BAM_FUNMAP) pre->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
if(!(pre->core.flag&BAM_FUNMAP)) sam_write1(out, header, pre);
if(!(cur->core.flag&BAM_FUNMAP)) sam_write1(out, header, cur);
}
has_prev = 0;
} else { // unpaired? clear bad info and write it out
if (pre->core.tid < 0 || pre->core.pos < 0 || pre->core.flag&BAM_FUNMAP) { // If unmapped
pre->core.flag |= BAM_FUNMAP;
pre->core.tid = -1;
pre->core.pos = -1;
}
pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
pre->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
if ( !remove_reads || !(pre->core.flag&BAM_FUNMAP) ) sam_write1(out, header, pre);
}
} else has_prev = 1;
curr = 1 - curr;
pre_end = cur_end;
}
if (has_prev && !remove_reads) { // If we still have a BAM in the buffer it must be unpaired
bam1_t *pre = b[1-curr];
if (pre->core.tid < 0 || pre->core.pos < 0 || pre->core.flag&BAM_FUNMAP) { // If unmapped
pre->core.flag |= BAM_FUNMAP;
pre->core.tid = -1;
pre->core.pos = -1;
}
pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
pre->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
sam_write1(out, header, pre);
}
bam_hdr_destroy(header);
bam_destroy1(b[0]);
bam_destroy1(b[1]);
free(str.s);
}
