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chhylp123
2024-11-12 23:53:29 -05:00
parent 6de4e14782
commit 80fa5ed436
11 changed files with 1211 additions and 135 deletions
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169
Process_Read.cpp
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@@ -51,6 +51,7 @@ void destory_All_reads(All_reads* r)
if (r->read_sperate[i]) free(r->read_sperate[i]);
if (r->paf && r->paf[i].buffer) free(r->paf[i].buffer);
if (r->reverse_paf && r->reverse_paf[i].buffer) free(r->reverse_paf[i].buffer);
if(r->rsc && r->rsc[i]) free(r->rsc[i]);
///if (r->pb_regions) kv_destroy(r->pb_regions[i].a);
}
free(r->paf);
@@ -61,6 +62,7 @@ void destory_All_reads(All_reads* r)
free(r->name_index);
free(r->read_length);
free(r->trio_flag);
free(r->rsc);
///if (r->pb_regions) free(r->pb_regions);
}
@@ -108,6 +110,14 @@ void write_All_reads(All_reads* r, char* read_file_name)
fwrite(&(asm_opt.hom_cov), sizeof(asm_opt.hom_cov), 1, fp);
fwrite(&(asm_opt.het_cov), sizeof(asm_opt.het_cov), 1, fp);
uint64_t mm = 1;
if(asm_opt.is_sc) {
fwrite(&mm, sizeof(mm), 1, fp);
for (i = 0; i < r->total_reads; i++) {
fwrite(r->rsc[i], sizeof(uint8_t), ((r->read_length[i]/sc_bn) + ((r->read_length[i]%sc_bn)?1:0)), fp);
}
}
free(index_name);
fflush(fp);
fclose(fp);
@@ -201,6 +211,19 @@ int load_All_reads(All_reads* r, char* read_file_name)
}
///r->pb_regions = NULL;
uint64_t mm = 0;
if (!feof(fp)) {
if((fread(&mm, sizeof(mm), 1, fp)) && (mm == 1)) {
MALLOC(r->rsc, r->total_reads);
for (i = 0; i < r->total_reads; i++) {
MALLOC(r->rsc[i], (r->read_length[i]/sc_bn) + ((r->read_length[i]%sc_bn)?1:0));
f_flag += fread(r->rsc[i], sizeof(uint8_t), (r->read_length[i]/sc_bn) + ((r->read_length[i]%sc_bn)?1:0), fp);
}
}
}
free(index_name);
fclose(fp);
fprintf(stderr, "Reads has been loaded.\n");
@@ -412,10 +435,13 @@ void malloc_All_reads(All_reads* r)
memcpy(r->read_size, r->read_length, sizeof(uint64_t)*r->total_reads);
r->read_sperate = (uint8_t**)malloc(sizeof(uint8_t*)*r->total_reads);
if(asm_opt.is_sc) MALLOC(r->rsc, r->total_reads);
long long i = 0;
for (i = 0; i < (long long)r->total_reads; i++)
{
r->read_sperate[i] = (uint8_t*)malloc(sizeof(uint8_t)*(r->read_length[i]/4+1));
if(r->rsc) MALLOC(r->rsc[i], (r->read_length[i]/sc_bn) + ((r->read_length[i]%sc_bn)?1:0));
}
r->cigars = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
@@ -823,6 +849,131 @@ void ha_compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_sit
}
}
void convert_qual(uint8_t* dest, char* src, uint64_t src_l, uint64_t bitu, uint64_t rev, uint64_t sc_off)
{
uint64_t i = 0; uint8_t c = 0, sc;
// fprintf(stderr, "\n[M::%s]\n", __func__);
for (i = 0; i < src_l; i++) {
for (c = 0, sc = ((uint8_t)src[i]) - sc_off; (c < bitu) && (sc_tb[c] < sc); c++);
if(c >= bitu) c = bitu - 1;
dest[(rev?(src_l-i-1):(i))] = c;
// fprintf(stderr, "%u->%u\n", sc, c);
}
}
void ha_compress_qual_bit(uint8_t* dest, char* src, uint64_t src_l, uint64_t bitn)
{
uint64_t i = 0, k, bit_r = 8/bitn, dest_i = 0;
uint8_t tmp = 0, c = 0;
for (i = 0; i + bit_r <= src_l;) {
for (k = tmp = 0; k < bit_r; k++) {
c = ((uint8_t)src[i]);
tmp <<= bitn; tmp |= c; i++;
}
dest[dest_i++] = tmp;
}
if(i < src_l) {
for (k = tmp = 0; i < src_l; k++) {
c = ((uint8_t)src[i]);
tmp <<= bitn; tmp |= c; i++;
}
dest[dest_i++] = (tmp<<(8-(bitn*k)));
}
}
void ha_compress_qual(uint8_t* dest, char* src, uint64_t src_l, uint64_t bitn, uint64_t sc_off)
{
uint64_t i = 0, k, bit_r = 8/bitn, dest_i = 0, bitu = (1<<bitn);
uint8_t tmp = 0, c = 0, sc;
for (i = 0; i + bit_r <= src_l;) {
for (k = tmp = 0; k < bit_r; k++) {
for (c = 0, sc = ((uint8_t)src[i]) - sc_off; (c < bitu) && (sc_tb[c] < sc); c++);
if(c >= bitu) c = bitu - 1;
tmp <<= bitn; tmp |= c; i++;
}
dest[dest_i++] = tmp;
}
if(i < src_l) {
for (k = tmp = 0; i < src_l; k++) {
for (c = 0, sc = ((uint8_t)src[i]) - sc_off; (c < bitu) && (sc_tb[c] < sc); c++);
if(c >= bitu) c = bitu - 1;
tmp <<= bitn; tmp |= c; i++;
}
dest[dest_i++] = (tmp<<(8-(bitn*k)));
}
}
///[s, e)
int64_t retrive_bqual(asg8_v *dv, uint8_t *ds, uint64_t id, int64_t s, int64_t e, uint8_t rev, int64_t bitn)
{
int64_t rl = Get_READ_LENGTH(R_INF, id), l;
if(s < 0) s = 0; if(e < 0) e = rl;
if(s >= e || e > rl) return -1;
uint8_t *da = NULL, *src = Get_QUAL(R_INF, id), mm = (((uint8_t)1)<<bitn)-1, mlf = 8 - bitn, mrf;
int64_t bitr = 8/bitn, dk, sk, swk;
l = e - s;
if(dv) {
kv_resize(uint8_t, *dv, ((uint64_t)l)); da = dv->a;
} else {
da = ds;
}
if(!rev) {
dk = 0; sk = s;
mrf = ((s%bitr)*bitn);
// if(s == 21519 && e == 22332) {
// fprintf(stderr, "+[M::%s] id::%lu, in::[%ld, %ld), rev::%u, bitn::%ld, bitr::%ld, mrf::%u\n", __func__, id, s, e, rev, bitn, bitr, mrf);
// }
if(mrf) {
for (swk = sk/bitr; mrf < 8 && sk < e; mrf += bitn, sk++) da[dk++] = ((src[swk]<<mrf)>>mlf)&mm;
}
for (swk = sk/bitr; (sk + bitr) <= e; sk += bitr, swk++) {
for (mrf = 0; mrf < 8; mrf += bitn) da[dk++] = ((src[swk]<<mrf)>>mlf)&mm;
}
if(sk < e) {
for (mrf = 0; sk < e; mrf += bitn, sk++) da[dk++] = ((src[swk]<<mrf)>>mlf)&mm;
}
// if(dk != l) {
// fprintf(stderr, "+[M::%s] id::%lu, in::[%ld, %ld), rev::%u, bitn::%ld, bitr::%ld\n", __func__, id, s, e, rev, bitn, bitr);
// }
assert(dk == l);
} else {
sk = s; s = e; e = sk;
s = rl - s; e = rl - e;
dk = l; sk = s;
mrf = ((s%bitr)*bitn);
if(mrf) {
for (swk = sk/bitr; mrf < 8 && sk < e; mrf += bitn, sk++) da[--dk] = ((src[swk]<<mrf)>>mlf)&mm;
}
for (swk = sk/bitr; (sk + bitr) <= e; sk += bitr, swk++) {
for (mrf = 0; mrf < 8; mrf += bitn) da[--dk] = ((src[swk]<<mrf)>>mlf)&mm;
}
if(sk < e) {
for (mrf = 0; sk < e; mrf += bitn, sk++) da[--dk] = ((src[swk]<<mrf)>>mlf)&mm;
}
assert(dk == 0);
}
dv->n = l;
return l;
}
void reverse_complement(char* pattern, uint64_t length)
{
uint64_t i = 0;
@@ -845,6 +996,24 @@ void reverse_complement(char* pattern, uint64_t length)
}
}
void print_fastq(FILE *fp, char *id, char *bs, char *qual, uint64_t bitu, uint64_t sc_off)
{
uint64_t i = 0, ql = strlen(qual); uint8_t c = 0, sc;
if(fp) fprintf(fp, "@%s\n%s\n+\n", id, bs);
else fprintf(stdout, "@%s\n%s\n+\n", id, bs);
for (i = 0; i < ql; i++) {
for (c = 0, sc = ((uint8_t)qual[i]) - sc_off; (c < bitu) && (sc_tb[c] < sc); c++);
if(c >= bitu) c = bitu - 1;
if(fp) fprintf(fp, "%u", c);
else fprintf(stdout, "%u", c);
}
if(fp) fprintf(fp, "\n");
else fprintf(stdout, "\n");
}
void init_Debug_reads(Debug_reads* x, const char* file)
{