static inline void
tmap_sam_print_fz_and_zf(tmap_file_t *fp, tmap_seq_t *seq)
{
uint16_t *flowgram = NULL;
int32_t flow_start_index;
int32_t flowgram_len;
flowgram_len = tmap_seq_get_flowgram(seq, &flowgram, 0);
if(NULL != flowgram) {
tmap_sam_print_flowgram(fp, flowgram, flowgram_len);
free(flowgram);
}
flow_start_index = tmap_seq_get_flow_start_index(seq);
if(0 <= flow_start_index) {
tmap_file_fprintf(fp, "\tZF:i:%d", flow_start_index);
}
}
void
tmap_seq_update(tmap_seq_t *seq, int32_t idx, sam_header_t *header)
{
char *rg_id = NULL;
sam_header_records_t *records = NULL;
sam_header_record_t **record_list = NULL;
int32_t n = 0;
// Read Group
switch(seq->type) {
case TMAP_SEQ_TYPE_FQ:
case TMAP_SEQ_TYPE_SFF:
break;
case TMAP_SEQ_TYPE_SAM:
case TMAP_SEQ_TYPE_BAM:
rg_id = tmap_sam_get_rg_id(seq->data.sam);
break;
default:
tmap_error("type is unrecognized", Exit, OutOfRange);
break;
}
if(NULL == rg_id) { // did not find in SAM/BAM
// NB: assume that it is from the ith record in the header
records = sam_header_get_records(header, "RG");
if(NULL != records) { // it exists
if(idx < 0 || records->n <= idx) {
tmap_error("RG records index was out of bounds", Exit, OutOfRange);
}
seq->rg_record = records->records[idx]; // copy over
if(NULL == seq->rg_record) tmap_bug();
}
}
else { // found in SAM/BAM
n = 0;
record_list = sam_header_get_record(header, "RG", "ID", rg_id, &n);
if(0 == n) {
fprintf(stderr, "Read Group Identifier: [%s]\n", rg_id);
tmap_error("Did not find the @RG.ID in the SAM/BAM Header", Exit, OutOfRange);
}
else if(1 < n) {
fprintf(stderr, "Read Group Identifier: [%s]\n", rg_id);
tmap_error("Found more than one @RG.ID in the SAM/BAM Header", Exit, OutOfRange);
}
seq->rg_record = record_list[0];
free(record_list); // NB: shallow copied
}
// Program Group
// NB: assumes the last item in the header
records = sam_header_get_records(header, "PG");
if(NULL != records && 0 < records->n) { // it exists
seq->pg_record = records->records[records->n-1]; // copy over
}
else {
seq->pg_record = NULL;
}
// key sequence and flow order
seq->fo_start_idx = -1;
if(NULL != seq->rg_record) { // It should exist in the SAM/BAM Header
seq->ks = sam_header_record_get(seq->rg_record, "KS");
seq->fo = sam_header_record_get(seq->rg_record, "FO");
// flow order index start
if(NULL != seq->ks && NULL != seq->fo && TMAP_SEQ_TYPE_SFF == seq->type) { // only if it is an SFF
// in addition, remove key sequence and trimming
seq->fo_start_idx = tmap_seq_remove_key_sequence(seq, 1);
}
else if(TMAP_SEQ_TYPE_SAM == seq->type || TMAP_SEQ_TYPE_BAM == seq->type) { // Try the ZF tag...
seq->fo_start_idx = tmap_sam_get_fo_start_idx(seq->data.sam);
}
// flowgram information...
seq->flowgram_len = tmap_seq_get_flowgram(seq, &seq->flowgram);
// check if all flowspace information is available
/*if((NULL == seq->ks || NULL == seq->fo || -1 == seq->fo_start_idx || NULL == seq->flowgram)// anything missing
&& (NULL != seq->ks || NULL != seq->fo || -1 != seq->fo_start_idx || NULL != seq->flowgram)) { // anything exists
fprintf(stderr, "@RG.KS %s present.\n", (NULL == seq->ks) ? "is not" : "is");
fprintf(stderr, "@RG.FO %s present.\n", (NULL == seq->fo) ? "is not" : "is");
fprintf(stderr, "@SAM.FZ %s present.\n", (NULL == seq->flowgram) ? "is not" : "is");
fprintf(stderr, "@SAM.ZF %s present.\n", (-1 == seq->fo_start_idx) ? "is not" : "is");
tmap_error("Not all flowspace information available (@RG.KS and @RG.FO, and @SAM.FZ and @SAM.ZF)", Exit, OutOfRange);
}*/
}
}
