int GetMultiSeq (InFileList *ifp, MULTISEQ *mseqs, const int pe, int(*get_read)(FILE * , seq_t * , const int)){
#ifdef DEBUG
// fprintf(stderr, "Get Multi Seqs\n");
#endif
ALNSEQ *alnSeq;
alnSeq= mseqs->seqList;
int num, len, id;
FILE * ifpA, * ifpB;
num = 0;
ifpA = ifp->ifpA; ifpB = ifp->ifpB;
id = ifp->id;
seq_t tmp;
tmp.max = tmp.l = 0;
tmp.seq = tmp.rc = tmp.qual = NULL;
while(num < MAX_MULTI_READS){
tmp.ns = 0;
if (feof(ifpA)||(pe && feof(ifpB))) break;
if ((len=get_read(ifpA, &tmp, TRUE))>0){
SEQDUP(alnSeq, tmp, pe);
++num;
if(pe &&(len=get_read(ifpB, &tmp, TRUE))>0){
SEQDUP(alnSeq, tmp, pe);
++num ;
}
++id;
}
}
mseqs->n = num;
ifp->id = id;
// fprintf(stderr, "%d\n", num);
/*
#ifdef DEBUG
int j;
fprintf(stderr, "len :%d\n", len);
fprintf(stderr, "fw\n");
for(j = 0; j<len; j++) fprintf(stderr, "%d", *(tmp.seq+j));
fprintf(stderr, "\n");
fprintf(stderr, "rc\n");
for(j = 0; j<len; j++) fprintf(stderr, "%d", *(tmp.rc+j));
fprintf(stderr, "\n");
alnSeq--;
for(j = 0; j < alnSeq->len; j++) fprintf(stderr, "rc %d", *(alnSeq->rc+j));
fprintf(stderr, "\n");
fprintf(stderr, "%s\n%s\n", alnSeq->name, alnSeq->qual);
fprintf(stderr, "soap get multisequences ...\n");
#endif
exit(0);
//*/
free(tmp.seq); free(tmp.qual);free(tmp.rc);
return num;
}
void read_sff_file(char* addr) {
sff_common_header* head = (sff_common_header*) addr;
if(ntohl(head->magic) != SFF_MAGIC) {
fprintf(stderr, "Warning: Bad magic number\n");
}
uint32_t nreads = ntohl(head->nreads);
uint16_t header_len = ntohs(head->header_len);
uint16_t flow_len = ntohs(head->flow_len);
char* current_addr = addr + header_len;
for(int i = 0; i < int(nreads); ++i) {
sff_read_header* read = (sff_read_header*) current_addr;
uint16_t rheader_len = ntohs(read->header_len);
uint32_t nbases = ntohl(read->nbases);
uint16_t name_len = ntohs(read->name_len);
uint16_t trim_left = ntohs(read->clip_qual_left) - 1; // these appear to be indexed from 1
uint16_t trim_right = ntohs(read->clip_qual_right) - 1;
/*
printf( "header_len = %d\n"
"name_len = %d\n"
"nbases = %d\n\n",
ntohs(read->header_len),
ntohs(read->name_len),
ntohl(read->nbases));
*/
get_read(current_addr + rheader_len, flow_len, nbases, trim_left, trim_right);
//exit(EXIT_SUCCESS);
current_addr = current_addr + rheader_len + pad((flow_len * 2) + (nbases * 3));
}
}
/*
* process one BAM record, and store accumulated results in 'results'
*/
int seqchksum_processRecord(bam1_t *rec, HASH_TYPE hash, chksum_results_t *results)
{
uint32_t crc = 0;
uint16_t aflags = rec->core.flag;
uint8_t *seq = get_read(rec);
uint8_t *qual = get_quality(rec);
uint16_t flag_mask = BAM_FPAIRED | BAM_FREAD1 | BAM_FREAD2;
uint8_t flags = (aflags & flag_mask) & 0xFF;
bool pass = !(aflags & BAM_FQCFAIL);;
char *qname = bam_get_qname(rec);
uint8_t *tag;
char *rgid;
HashItem *hi;
HashData hd;
int newitem;
digest_line_t *dline_all;
digest_line_t *dline;
// look up the RG tag
tag = bam_aux_get(rec, "RG");
//hd.p = malloc(sizeof(digest_line_t));
if (tag) rgid = bam_aux2Z(tag);
else rgid = "";
hd.p = NULL;
hi = HashTableAdd(results->rgHash, rgid, 0, hd, &newitem);
if (newitem) {
hi->data.p = malloc(sizeof(digest_line_t));
dline = hi->data.p;
init_digest_line(hash,dline);
} else {
dline = hi->data.p;
}
dline_all = &(results->all);
// flags + sequence chksum
update_crc(&crc,&flags,1);
update_crc(&crc,seq,strlen((char*)seq));
update_digest_line(hash, pass, dline, crc, 0);
update_digest_line(hash, pass, dline_all, crc, 0);
// flags + sequence + quality chksum (don't reset crc, just add quality)
update_crc(&crc,qual,strlen((char*)qual));
update_digest_line(hash, pass, dline, crc, 2);
update_digest_line(hash, pass, dline_all, crc, 2);
// name + flags + sequence chksum
crc = 0;
update_crc(&crc, (uint8_t *)qname, strlen(qname)+1);
update_crc(&crc, &flags, 1);
update_crc(&crc,seq,strlen((char*)seq));
update_digest_line(hash, pass, dline, crc, 1);
update_digest_line(hash, pass, dline_all, crc, 1);
// flags + sequence + tags chksum
crc = 0;
update_crc(&crc, &flags, 1);
update_crc(&crc,seq,strlen((char*)seq));
tag = bam_aux_get(rec,"BC"); if (tag) update_crc(&crc,tag-2,aux_type2size(tag)+3);
tag = bam_aux_get(rec,"FI"); if (tag) update_crc(&crc,tag-2,aux_type2size(tag)+3);
tag = bam_aux_get(rec,"QT"); if (tag) update_crc(&crc,tag-2,aux_type2size(tag)+3);
tag = bam_aux_get(rec,"RT"); if (tag) update_crc(&crc,tag-2,aux_type2size(tag)+3);
tag = bam_aux_get(rec,"TC"); if (tag) update_crc(&crc,tag-2,aux_type2size(tag)+3);
update_digest_line(hash, pass, dline, crc, 3);
update_digest_line(hash, pass, dline_all, crc, 3);
free(seq); free(qual);
return 0;
}
