void
tmap_sff_reverse(tmap_sff_t *sff)
{
uint32_t i;
// reverse flowgram
for(i=0;i<(sff->gheader->flow_length>>1);i++) {
uint16_t tmp = sff->read->flowgram[sff->gheader->flow_length-1-i];
sff->read->flowgram[sff->gheader->flow_length-1-i] = sff->read->flowgram[i];
sff->read->flowgram[i] = tmp;
}
// reverse flow index
for(i=0;i<(sff->rheader->n_bases>>1);i++) {
uint8_t tmp = sff->read->flow_index[sff->rheader->n_bases-1-i];
sff->read->flow_index[sff->rheader->n_bases-1-i] = sff->read->flow_index[i];
sff->read->flow_index[i] = tmp;
}
// reverse compliment the bases
tmap_string_reverse(sff->read->bases);
// reverse the qualities
tmap_string_reverse(sff->read->quality);
}
void
tmap_sam_reverse_compliment(tmap_sam_t *sam)
{
tmap_string_reverse_compliment(sam->seq, sam->is_int);
tmap_string_reverse(sam->qual);
}
void
tmap_sam_reverse(tmap_sam_t *sam)
{
tmap_string_reverse(sam->seq);
tmap_string_reverse(sam->qual);
}
void
tmap_fq_reverse_compliment(tmap_fq_t *fq)
{
tmap_string_reverse_compliment(fq->seq, fq->is_int);
tmap_string_reverse(fq->qual);
}
void
tmap_fq_reverse(tmap_fq_t *fq)
{
tmap_string_reverse(fq->seq);
tmap_string_reverse(fq->qual);
}
inline void
tmap_sam_print_mapped(tmap_file_t *fp, tmap_seq_t *seq, int32_t sam_flowspace_tags, int32_t bidirectional, int32_t seq_eq, tmap_refseq_t *refseq,
uint8_t strand, uint32_t seqid, uint32_t pos, int32_t aln_num,
uint32_t end_num, uint32_t m_unmapped, uint32_t m_prop, double m_num_std, uint32_t m_strand,
uint32_t m_seqid, uint32_t m_pos, uint32_t m_tlen,
uint8_t mapq, uint32_t *cigar, int32_t n_cigar,
int32_t score, int32_t ascore, int32_t pscore, int32_t nh, int32_t algo_id, int32_t algo_stage,
const char *format, ...)
{
va_list ap;
int32_t i;
tmap_string_t *name=NULL, *bases=NULL, *qualities=NULL;
char *bases_eq=NULL;
uint32_t flag;
tmap_string_t *md;
int32_t nm;
/*
fprintf(stderr, "end_num=%d m_unmapped=%d m_prop=%d m_strand=%d m_seqid=%d m_pos=%d m_tlen=%d\n",
end_num, m_unmapped, m_prop, m_strand, m_seqid, m_pos, m_tlen);
*/
name = tmap_seq_get_name(seq);
bases = tmap_seq_get_bases(seq);
qualities = tmap_seq_get_qualities(seq);
if(1 == strand) { // reverse for the output
tmap_string_reverse_compliment(bases, 0);
tmap_string_reverse(qualities);
}
if(0 == pos + 1) {
tmap_error("position is out of range", Exit, OutOfRange);
}
// compute the MD/NM
if(1 == seq_eq && 0 < bases->l) {
bases_eq = tmap_calloc((1 + bases->l), sizeof(char), "bases_eq");
}
else {
bases_eq = NULL;
}
md = tmap_sam_md(refseq, bases->s, seqid, pos, cigar, n_cigar, &nm, bases_eq);
// flag
flag = 0;
if(1 == strand) flag |= 0x10; // strand
if(0 < aln_num) flag |= 0x100; // secondary alignment
if(0 < end_num) { // mate info
flag |= 0x1;
if(0 == m_unmapped && 1 == m_prop) flag |= 0x2; // properly aligned
if(1 == m_unmapped) flag |= 0x8; // unmapped
else if(1 == m_strand) flag |= 0x20; // strand
flag |= (1 == end_num) ? 0x40 : 0x80; // first/second end
}
tmap_file_fprintf(fp, "%s\t%u\t%s\t%u\t%u\t",
name->s, flag, refseq->annos[seqid].name->s,
pos + 1,
mapq);
// print out the cigar
if(TMAP_SEQ_TYPE_SFF == seq->type) {
if(0 == strand && 0 < seq->data.sff->rheader->clip_left) {
tmap_file_fprintf(fp, "%dH", seq->data.sff->rheader->clip_left);
}
else if(1 == strand && 0 < seq->data.sff->rheader->clip_right) {
tmap_file_fprintf(fp, "%dH", seq->data.sff->rheader->clip_right);
}
}
for(i=0;i<n_cigar;i++) {
tmap_file_fprintf(fp, "%d%c",
cigar[i]>>4, "MIDNSHP"[cigar[i]&0xf]);
}
if(TMAP_SEQ_TYPE_SFF == seq->type) {
if(1 == strand && 0 < seq->data.sff->rheader->clip_left) {
tmap_file_fprintf(fp, "%dH", seq->data.sff->rheader->clip_left);
}
else if(0 == strand && 0 < seq->data.sff->rheader->clip_right) {
tmap_file_fprintf(fp, "%dH", seq->data.sff->rheader->clip_right);
}
}
// mate info
if(0 == end_num) { // no mate
tmap_file_fprintf(fp, "\t*\t0\t0");
}
else if(1 == m_unmapped) { // unmapped mate
tmap_file_fprintf(fp, "\t%s\t%u\t%u",
"=",
pos + 1,
0);
}
else { // mapped mate
tmap_file_fprintf(fp, "\t%s\t%u\t%d",
refseq->annos[m_seqid].name->s,
m_pos+1,
m_tlen);
}
// bases and qualities
if(1 == seq_eq && NULL != bases_eq) {
tmap_file_fprintf(fp, "\t%s\t%s", bases_eq, (0 == qualities->l) ? "*" : qualities->s);
}
else {
tmap_file_fprintf(fp, "\t%s\t%s", bases->s, (0 == qualities->l) ? "*" : qualities->s);
}
// RG
tmap_sam_print_rg(fp, seq);
// PG
tmap_file_fprintf(fp, "\tPG:Z:%s", PACKAGE_NAME);
// MD and NM
tmap_file_fprintf(fp, "\tMD:Z:%s\tNM:i:%d", md->s, nm);
// AS
tmap_file_fprintf(fp, "\tAS:i:%d", score);
// NH
if(1 < nh) tmap_file_fprintf(fp, "\tNH:i:%d", nh);
// FZ and ZF
if(1 == sam_flowspace_tags) {
tmap_sam_print_fz_and_zf(fp, seq);
}
// XA
if(0 < algo_stage) {
tmap_file_fprintf(fp, "\tXA:Z:%s-%d", tmap_algo_id_to_name(algo_id), algo_stage);
}
// XZ
if(TMAP_SEQ_TYPE_SFF == seq->type && INT32_MIN != ascore) {
tmap_file_fprintf(fp, "\tXZ:i:%d", ascore);
}
if(0 < end_num) { // mate info
tmap_file_fprintf(fp, "\tYP:i:%d", pscore);
if(0 == m_unmapped) {
tmap_file_fprintf(fp, "\tYS:f:%f", m_num_std);
}
}
if(1 == bidirectional) {
tmap_file_fprintf(fp, "\tXB:i:1");
}
// optional tags
if(NULL != format) {
va_start(ap, format);
tmap_file_vfprintf(fp, format, ap);
va_end(ap);
}
// new line
tmap_file_fprintf(fp, "\n");
if(1 == strand) { // reverse back
tmap_string_reverse_compliment(bases, 0);
tmap_string_reverse(qualities);
}
// free
tmap_string_destroy(md);
free(bases_eq);
}
