void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
{
bam1_t *swap;
int i, end;
uint32_t *cigar;
str->l = 0;
if (b1->core.tid != b2->core.tid || b1->core.tid < 0) return; // coordinateless or not on the same chr; skip
if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate
kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
for (i = 0, cigar = bam1_cigar(b1); i < b1->core.n_cigar; ++i) {
kputw(bam_cigar_oplen(cigar[i]), str);
kputc(bam_cigar_opchr(cigar[i]), str);
}
end = bam_calend(&b1->core, cigar);
kputw(b2->core.pos - end, str);
kputc('T', str);
kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
for (i = 0, cigar = bam1_cigar(b2); i < b2->core.n_cigar; ++i) {
kputw(bam_cigar_oplen(cigar[i]), str);
kputc(bam_cigar_opchr(cigar[i]), str);
}
bam_aux_append(b1, "CT", 'Z', str->l+1, (uint8_t*)str->s);
}
/*
* This function calculates ct tag for two bams, it assumes they are from the same template and
* writes the tag to the first read in position terms.
*/
static void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
{
bam1_t *swap;
int i, end;
uint32_t *cigar;
str->l = 0;
if (b1->core.tid != b2->core.tid || b1->core.tid < 0 || b1->core.pos < 0 || b2->core.pos < 0 || b1->core.flag&BAM_FUNMAP || b2->core.flag&BAM_FUNMAP) return; // coordinateless or not on the same chr; skip
if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate
kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
for (i = 0, cigar = bam_get_cigar(b1); i < b1->core.n_cigar; ++i) {
kputw(bam_cigar_oplen(cigar[i]), str);
kputc(bam_cigar_opchr(cigar[i]), str);
}
end = bam_endpos(b1);
kputw(b2->core.pos - end, str);
kputc('T', str);
kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
for (i = 0, cigar = bam_get_cigar(b2); i < b2->core.n_cigar; ++i) {
kputw(bam_cigar_oplen(cigar[i]), str);
kputc(bam_cigar_opchr(cigar[i]), str);
}
uint8_t* data;
if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data);
if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data);
bam_aux_append(b1, "ct", 'Z', str->l+1, (uint8_t*)str->s);
}
void calcAlnOffsets(uint32_t *cigar,
uint32_t n_cigar,
uint32_t sa_pos,
char sa_strand,
struct line *l)
{
l->raLen = 0;
l->qaLen = 0;
l->sclip = 0;
l->eclip = 0;
l->SQO = 0;
l->EQO = 0;
bool first = true;
uint32_t k;
for (k = 0; k < n_cigar; ++k)
{
uint32_t opLen = bam_cigar_oplen(cigar[k]);
char opCode = bam_cigar_opchr(cigar[k]);
if (opCode == 'M' || opCode == '=' || opCode == 'X')
{
l->raLen += opLen;
l->qaLen += opLen;
first = false;
}
else if (opCode == 'S' || opCode == 'H')
{
if (first) l->sclip += opLen;
else l->eclip += opLen;
}
else if (opCode == 'D' || opCode == 'N')
{
l->raLen += opLen;
}
else if (opCode == 'I')
{
l->qaLen += opLen;
}
}
//*rapos = str2pos(line->fields[POS]);
l->rapos = sa_pos;
if (sa_strand == '+')
{
l->pos = l->rapos - l->sclip;
l->SQO = l->sclip;
l->EQO = l->sclip + l->qaLen - 1;
}
else
{
l->pos = l->rapos + l->raLen + l->eclip - 1;
l->SQO = l->eclip;
l->EQO = l->eclip + l->qaLen - 1;
}
}
// Adapted from samtools/bam.c
int32_t b2g_bam_clippedlength(bam1_t *b) {
const bam1_core_t c = b->core;
const uint32_t *cigar = bam1_cigar(b);
uint32_t k;
int32_t l = 0;
for (k = 0; k < c.n_cigar; ++k) {
if ('S' == bam_cigar_opchr(bam_cigar_op(cigar[k]))) {
l += bam_cigar_oplen(cigar[k]);
}
}
return l;
}
/**
* Gets the cigar from a BAM record
*/
void bam_get_cigar_string(bam1_t *s, kstring_t *cigar_string)
{
cigar_string->l=0;
int32_t n_cigar_op = bam_get_n_cigar_op(s);
if (n_cigar_op)
{
uint32_t *cigar = bam_get_cigar(s);
for (int32_t i = 0; i < n_cigar_op; ++i)
{
kputw(bam_cigar_oplen(cigar[i]), cigar_string);
kputc(bam_cigar_opchr(cigar[i]), cigar_string);
}
}
}
static int32_t unclipped_start(bam1_t *b) {
uint32_t *cigar = bam_get_cigar(b);
int32_t clipped = 0;
uint32_t i;
for (i = 0; i < b->core.n_cigar; i++) {
char c = bam_cigar_opchr(cigar[i]);
if (c == 'S' || c == 'H') { // clips
clipped += bam_cigar_oplen(cigar[i]);
} else {
break;
}
}
return b->core.pos - clipped + 1;
}
// Returns 0 on success, -1 on failure.
static int bam_format_cigar(const bam1_t* b, kstring_t* str)
{
// An empty cigar is a special case return "*" rather than ""
if (b->core.n_cigar == 0) {
return (kputc('*', str) == EOF) ? -1 : 0;
}
const uint32_t *cigar = bam_get_cigar(b);
uint32_t i;
for (i = 0; i < b->core.n_cigar; ++i) {
if (kputw(bam_cigar_oplen(cigar[i]), str) == EOF) return -1;
if (kputc(bam_cigar_opchr(cigar[i]), str) == EOF) return -1;
}
return 0;
}
static int32_t unclipped_end(bam1_t *b) {
uint32_t *cigar = bam_get_cigar(b);
int32_t end_pos, clipped = 0;
int32_t i;
end_pos = bam_endpos(b);
// now get the clipped end bases (if any)
// if we get to the beginning of the cigar string
// without hitting a non-clip then the results are meaningless
for (i = b->core.n_cigar - 1; i >= 0; i--) {
char c = bam_cigar_opchr(cigar[i]);
if (c == 'S' || c == 'H') { // clips
clipped += bam_cigar_oplen(cigar[i]);
} else {
break;
}
}
return end_pos + clipped;
}
string bam_cigarString (bam1_t *b) {//output CIGAR string
// kstring_t strK;
// kstring_t *str=&strK;
const bam1_core_t *c = &b->core;
string cigarString("");
if ( c->n_cigar > 0 ) {
uint32_t *cigar = bam_get_cigar(b);
for (int i = 0; i < c->n_cigar; ++i) {
cigarString+=to_string((uint)bam_cigar_oplen(cigar[i]))+bam_cigar_opchr(cigar[i]);
};
};
// if (c->n_cigar) { // cigar
// for (int i = 0; i < c->n_cigar; ++i) {
// kputw(bam_cigar_oplen(cigar[i]), str);
// kputc(bam_cigar_opchr(cigar[i]), str);
// }
// } else kputc('*', str);
//
// string cigarString (str->s,str->l);
return cigarString;
};
int do_grep() {
#ifdef DEBUGa
printf("[!]do_grep\n");
#endif
BamInfo_t *pbam;
kh_cstr_t BamID;
khiter_t ki, bami;
kstring_t ks1 = { 0, 0, NULL };
kstring_t ks2 = { 0, 0, NULL };
kstring_t ks3 = { 0, 0, NULL };
samFile *in;
bam_hdr_t *h;
hts_idx_t *idx;
bam1_t *b, *d, *d2, *bR1, *bR2, *bR3;
bR1 = bam_init1(); bR2 = bam_init1(); bR3 = bam_init1();
//htsFile *out;
//hts_opt *in_opts = NULL, *out_opts = NULL;
int r = 0, exit_code = 0;
kvec_t(bam1_t) R1, R2, RV;
pierCluster_t *pierCluster;
//samdat_t tmp_samdat;
FILE *fs = fopen("./test.txt","w");
for (bami = kh_begin(bamNFOp); bami != kh_end(bamNFOp); ++bami) {
//printf(">[%d]:\n",bami);
if (kh_exist(bamNFOp, bami)) {
kv_init(R1); kv_init(R2); kv_init(RV);
//tmp_samdat = (const samdat_t){ 0 };
//memset(&tmp_samdat,0,sizeof(samdat_t));
//printf("-[%d]:\n",bami);
BamID = kh_key(bamNFOp, bami);
pbam = &kh_value(bamNFOp, bami);
fprintf(stderr, "%u [%s]=%s\t%u %u\n",bami,BamID,pbam->fileName,pbam->insertSize,pbam->SD);
in = sam_open(pbam->fileName, "r");
if (in == NULL) {
fprintf(stderr, "[x]Error opening \"%s\"\n", pbam->fileName);
return EXIT_FAILURE;
}
h = sam_hdr_read(in);
/* out = hts_open("-", "w");
if (out == NULL) {
fprintf(stderr, "[x]Error opening standard output\n");
return EXIT_FAILURE;
}
if (sam_hdr_write(out, h) < 0) {
fprintf(stderr, "[!]Error writing output header.\n");
exit_code = 1;
}
*/
int8_t *ChrIsHum;
if (h == NULL) {
fprintf(stderr, "[x]Couldn't read header for \"%s\"\n", pbam->fileName);
return EXIT_FAILURE;
} else {
ChrIsHum = malloc(h->n_targets * sizeof(int8_t));
for (int32_t i=0; i < h->n_targets; ++i) {
//ChrIsHum[i] = -1;
ki = kh_get(chrNFO, chrNFOp, h->target_name[i]);
if (ki == kh_end(chrNFOp)) {
errx(4,"[x]Cannot find ChrID for [%s] !",h->target_name[i]);
} else {
ChrInfo_t * tmp = &kh_value(chrNFOp, ki);
ChrIsHum[i] = tmp->isHum;
//printf(">>> %d Chr:%s %d\n",i,h->target_name[i],ChrIsHum[i]);
}
}
}
h->ignore_sam_err = 0;
b = bam_init1();
d = bam_init1();
d2 = bam_init1();
if ((idx = sam_index_load(in, pbam->fileName)) == 0) {
fprintf(stderr, "[E::%s] fail to load the BAM index\n", __func__);
return 1;
}
pierCluster = sam_plp_init();
while ((r = sam_read1(in, h, b)) >= 0) {
int8_t flag = false;
const bam1_core_t *c = &b->core;
if (c->flag & BAM_FSECONDARY) continue;
if (c->n_cigar) {
uint32_t *cigar = bam_get_cigar(b);
for (int i = 0; i < c->n_cigar; ++i) {
if (bam_cigar_opchr(cigar[i])=='S') { // soft clipping
if ( bam_cigar_oplen(cigar[i]) >= myConfig.minGrepSlen ) {
flag = true;
}
}
}
}
if (flag && ChrIsHum[c->tid]) { // Now, skip Virus items.
//bam_copy1(bR1, b);
flag = 0; // recycle
//int enoughMapQ = 0;
//kstring_t ks = { 0, 0, NULL };
/*if (sam_format1(h, b, &ks1) < 0) {
fprintf(stderr, "Error writing output.\n");
exit_code = 1;
break;
} else*/ if ((c->mtid == c->tid && ChrIsHum[c->tid]) || (ChrIsHum[c->tid] ^ ChrIsHum[c->mtid])) { // Only grep those mapped on same Human ChrID, or diff species/一方在病毒的情况.
//printf(">[%s]\n",ks_str(&ks1));
flag |= 1;
//tmp_samdat.b = bam_dup1(b);
//kv_push(samdat_t,R1,tmp_samdat);
/*if (checkMapQ(ChrIsHum, b, true)) {
++enoughMapQ;
}*/
}
if (getPairedSam(in, idx, b, d) != 0) {
flag &= ~1;
continue;
} else {
flag |= 2;
/*if (checkMapQ(ChrIsHum, d, false)) {
++enoughMapQ;
}*/
/*if (c->flag & BAM_FSECONDARY) {
if (getPairedSam(in, idx, d, d2) == 0) {
//sam_format1(h, d2, &ks3);
flag |= 4;
if (checkMapQ(ChrIsHum, d2, false)) {
++enoughMapQ;
}
}
}*/
}
/*
对于 BAM_FSECONDARY(256) 的 Read，跳两次 与 读 SA 项，效果一样。
>[sf95_Ref_48245009_48245108_48245208_Vir_-_2000_2044_R_100_90 353 chr2 13996555 0 50S40M chr18 48245109 0ACACAACAATGTTCCGGAGACTCTAAGGCCTCCCGATACAGAGCAGAGGCCACACACACACACACCATGGAATACTATTCAGCCAAAAAA CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC NM:i:0 MD:Z:40 AS:i:40 XS:i:40 RG:Z:Fsimout_mB SA:Z:rgi|59585|emb|X04615.1|,2000,-,40S46M4S,60,0; YC:Z:CT YD:Z:f]
-[sf95_Ref_48245009_48245108_48245208_Vir_-_2000_2044_R_100_90 177 chr18 48245109 9 40S50M gi|59585|emb|X04615.1|2000 0 GTTCCGGAGACTCTAAGGCCTCCCGATACAGAGCAGAGGCCACACACACACACACCATGGAATACTATTCAGCCAAAAAAAGGAATTCAA CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC NM:i:0 MD:Z:50 AS:i:50 XS:i:46 RG:Z:Fsimout_mB SA:Z:rgi|59585|emb|X04615.1|,2000,+,50S40M,9,0; YC:Z:GA YD:Z:f]
+[sf95_Ref_48245009_48245108_48245208_Vir_-_2000_2044_R_100_90 113 gi|59585|emb|X04615.1| 2000 60 40S46M4S chr18 48245109 0 TTTTTTGGCTGAATAGTATTCCATGGTGTGTGTGTGTGTGGCCTCTGCTCTGTATCGGGAGGCCTTAGAGTCTCCGGAACATTGTTGTGT CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC NM:i:0 MD:Z:46 AS:i:46 XS:i:27 RG:Z:Fsimout_mB SA:Z:fchr2,13996555,+,50S40M,0,0; YC:Z:CT YD:Z:r]
*/
/*if (sam_format1(h, d, &ks2) < 0) {
fprintf(stderr, "Error writing output.\n");
exit_code = 1;
break;
}*/
if (((flag & 3) == 3) /*&& enoughMapQ >= myConfig.samples*/) {
/*printf(">%d[%s]\n",checkMapQ(ChrIsHum, b, true),ks_str(&ks1));
printf("-%d[%s]\n",checkMapQ(ChrIsHum, d, false),ks_str(&ks2));
if (flag & 4) {
printf("+%d[%s]\n",checkMapQ(ChrIsHum, d2, false),ks_str(&ks3));
}
printf("<--%d\n",enoughMapQ);*/
if (sam_plp_push(ChrIsHum, pierCluster, b) == 0) {
//printf("--HumRange=%s:%d-%d\n", h->target_name[(pierCluster->HumanRange).tid], (pierCluster->HumanRange).pos, (pierCluster->HumanRange).endpos);
if ((!ChrIsHum[(d->core).tid]) && (flag & 2)) sam_plp_push(ChrIsHum, pierCluster, d);
//if ((!ChrIsHum[(d2->core).tid]) && (flag & 4)) sam_plp_push(ChrIsHum, pierCluster, d2);
} else {
//print
fprintf(fs,"[%s]\nHumRange=%s:%d-%d\n", BamID, h->target_name[(pierCluster->HumanRange).tid], (pierCluster->HumanRange).pos, (pierCluster->HumanRange).endpos);
fprintf(fs,"VirRange=%s:%d-%d\n", h->target_name[(pierCluster->VirusRange).tid], (pierCluster->VirusRange).pos, (pierCluster->VirusRange).endpos);
for (size_t i=0; i<kv_size(pierCluster->Reads);++i) {
bam1_t *bi = kv_A(pierCluster->Reads, i);
if (sam_format1(h, bi, &ks1) < 0) {
fprintf(stderr, "Error writing output.\n");
exit_code = 1;
break;
} else {
fprintf(fs,"%s\n",ks1.s);
}
}
fprintf(fs,"\n");
//printf("HumRange=%s:%d-%d\n", h->target_name[(pierCluster->HumanRange).tid], (pierCluster->HumanRange).pos, (pierCluster->HumanRange).endpos);
//fflush(fs);
sam_plp_dectroy(pierCluster);
pierCluster = sam_plp_init();
}
}
}
/*char *qname = bam_get_qname(b);
if (sam_write1(out, h, b) < 0) {
fprintf(stderr, "[x]Error writing output.\n");
exit_code = 1;
break;
}*/
}
/* r = sam_close(out); // stdout can only be closed once
if (r < 0) {
fprintf(stderr, "Error closing output.\n");
exit_code = 1;
}
*/
hts_idx_destroy(idx);
bam_destroy1(b);
bam_destroy1(d);
bam_destroy1(d2);
bam_hdr_destroy(h);
r = sam_close(in);
free(ChrIsHum);
#ifdef DEBUGa
fflush(NULL);
//pressAnyKey();
#endif
sam_plp_dectroy(pierCluster);
//printf("<[%d]:\n",bami);
}
}
fclose(fs);
getPairedSam(NULL, NULL, NULL, NULL); // sam_close(fp2);
//printf("---[%d]---\n",exit_code);
bam_destroy1(bR1); bam_destroy1(bR2); bam_destroy1(bR3);
ks_release(&ks1);
ks_release(&ks2);
ks_release(&ks3);
return exit_code;
}
char CigarOperation::TypeToChar(const CigarOperationType type)
{ return bam_cigar_opchr(static_cast<int>(type)); }
/**
* Gets the base in the read that is mapped to a genomic position.
* Extracts the read sequence and aualities too.
*/
void bam_get_base_and_qual_and_read_and_qual(bam1_t *srec, uint32_t pos, char& base, char& qual, int32_t& rpos, kstring_t* readseq, kstring_t* readqual)
{
bam1_core_t *c = &srec->core;
int32_t rlen = c->l_qseq;
uint32_t cpos = c->pos; //reference coordinates of the first mapped base
rpos = 0; //read coordinates
kstring_t str;
str.l = str.m = 0, str.s = 0;
base = 'N';
qual = 0;
if (c->n_cigar)
{
uint32_t *cigar = bam_get_cigar(srec);
for (uint32_t i = 0; i < c->n_cigar; ++i)
{
char op = bam_cigar_opchr(cigar[i]);
str.l = 0;
kputw(bam_cigar_oplen(cigar[i]), &str);
char* stop;
uint32_t len = strtol(str.s, &stop, 10);
assert(stop);
if (op=='M')
{
if (pos>=cpos && pos<=cpos+len-1)
{
rpos += pos-cpos;
break;
}
cpos += len;
rpos += len;
}
else if (op=='D')
{
if (pos>=cpos && pos<=cpos+len-1)
{
rpos = -1;
break;
}
cpos += len;
}
else if (op=='S' || op=='I')
{
rpos += len;
}
}
//std::cout << "bpos " << bpos << "\n";
if (rpos>=0 && rpos<=rlen)
{
//sequence
bam_get_seq_string(srec, readseq);
base = readseq->s[rpos];
//qual
bam_get_qual_string(srec, readqual);
qual = readqual->s[rpos];
}
else
{
rpos = BAM_READ_INDEX_NA;
}
}
// std::cout << "b: " << base << "\n";
// std::cout << "q: " << s[bpos-1] << " " << q << "\n";
// for (uint32_t i = 0; i < c->l_qseq; ++i) std::cerr << ((char)(s[i] + 33));
};
