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@jkbonfield
jkbonfield committed May 14, 2024
1 parent c918409 commit 84bbe2c
Showing 1 changed file with 34 additions and 44 deletions.
78 changes: 34 additions & 44 deletions sam.c
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Original file line number Diff line number Diff line change
Expand Up @@ -774,16 +774,16 @@ static int fixup_missing_qname_nul(bam1_t *b) {
* Note a second interface that returns a bam pointer instead would avoid bam_copy1
* in multi-threaded handling. This may be worth considering for htslib2.
*/
#define bgzf_read bgzf_read_small
int bam_read1(BGZF *fp, bam1_t *b)
{
bam1_core_t *c = &b->core;
int32_t block_len, ret, i;
uint32_t x[8], new_l_data;
uint32_t new_l_data;
uint8_t tmp[32], *x;

b->l_data = 0;

if ((ret = bgzf_read(fp, &block_len, 4)) != 4) {
if ((ret = bgzf_read_small(fp, &block_len, 4)) != 4) {
if (ret == 0) return -1; // normal end-of-file
else return -2; // truncated
}
Expand All @@ -792,34 +792,27 @@ int bam_read1(BGZF *fp, bam1_t *b)
if (block_len < 32) return -4; // block_len includes core data
if (fp->block_length - fp->block_offset > 32) {
// Avoid bgzf_read and a temporary copy to a local buffer
uint8_t *x = (uint8_t *)fp->uncompressed_block + fp->block_offset;
c->tid = le_to_u32(x);
c->pos = le_to_i32(x+4);
uint32_t x2 = le_to_u32(x+8);
c->bin = x2>>16;
c->qual = x2>>8&0xff;
c->l_qname = x2&0xff;
c->l_extranul = (c->l_qname%4 != 0)? (4 - c->l_qname%4) : 0;
uint32_t x3 = le_to_u32(x+12);
c->flag = x3>>16;
c->n_cigar = x3&0xffff;
c->l_qseq = le_to_u32(x+16);
c->mtid = le_to_u32(x+20);
c->mpos = le_to_i32(x+24);
c->isize = le_to_i32(x+28);
x = (uint8_t *)fp->uncompressed_block + fp->block_offset;
fp->block_offset += 32;
} else {
if (bgzf_read(fp, &x, 32) != 32) return -3;
if (fp->is_be) {
for (i = 0; i < 8; ++i) ed_swap_4p(x + i);
}
c->tid = x[0]; c->pos = (int32_t)x[1];
c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
c->l_extranul = (c->l_qname%4 != 0)? (4 - c->l_qname%4) : 0;
c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
c->l_qseq = x[4];
c->mtid = x[5]; c->mpos = (int32_t)x[6]; c->isize = (int32_t)x[7];
}
x = tmp;
if (bgzf_read(fp, x, 32) != 32) return -3;
}

c->tid = le_to_u32(x);
c->pos = le_to_i32(x+4);
uint32_t x2 = le_to_u32(x+8);
c->bin = x2>>16;
c->qual = x2>>8&0xff;
c->l_qname = x2&0xff;
c->l_extranul = (c->l_qname%4 != 0)? (4 - c->l_qname%4) : 0;
uint32_t x3 = le_to_u32(x+12);
c->flag = x3>>16;
c->n_cigar = x3&0xffff;
c->l_qseq = le_to_u32(x+16);
c->mtid = le_to_u32(x+20);
c->mpos = le_to_i32(x+24);
c->isize = le_to_i32(x+28);

new_l_data = block_len - 32 + c->l_extranul;
if (new_l_data > INT_MAX || c->l_qseq < 0 || c->l_qname < 1) return -4;
Expand All @@ -829,14 +822,14 @@ int bam_read1(BGZF *fp, bam1_t *b)
if (realloc_bam_data(b, new_l_data) < 0) return -4;
b->l_data = new_l_data;

if (bgzf_read(fp, b->data, c->l_qname) != c->l_qname) return -4;
if (bgzf_read_small(fp, b->data, c->l_qname) != c->l_qname) return -4;
if (b->data[c->l_qname - 1] != '\0') { // try to fix missing nul termination
if (fixup_missing_qname_nul(b) < 0) return -4;
}
for (i = 0; i < c->l_extranul; ++i) b->data[c->l_qname+i] = '\0';
c->l_qname += c->l_extranul;
if (b->l_data < c->l_qname ||
bgzf_read(fp, b->data + c->l_qname, b->l_data - c->l_qname) != b->l_data - c->l_qname)
bgzf_read_small(fp, b->data + c->l_qname, b->l_data - c->l_qname) != b->l_data - c->l_qname)
return -4;
if (fp->is_be) swap_data(c, b->l_data, b->data, 0);
if (bam_tag2cigar(b, 0, 0) < 0)
Expand All @@ -858,9 +851,7 @@ int bam_read1(BGZF *fp, bam1_t *b)

return 4 + block_len;
}
#undef bgzf_read

#define bgzf_write bgzf_write_small
int bam_write1(BGZF *fp, const bam1_t *b)
{
const bam1_core_t *c = &b->core;
Expand Down Expand Up @@ -891,15 +882,15 @@ int bam_write1(BGZF *fp, const bam1_t *b)
if (fp->is_be) {
for (i = 0; i < 8; ++i) ed_swap_4p(x + i);
y = block_len;
if (ok) ok = (bgzf_write(fp, ed_swap_4p(&y), 4) >= 0);
if (ok) ok = (bgzf_write_small(fp, ed_swap_4p(&y), 4) >= 0);
swap_data(c, b->l_data, b->data, 1);
} else {
if (ok) ok = (bgzf_write(fp, &block_len, 4) >= 0);
if (ok) ok = (bgzf_write_small(fp, &block_len, 4) >= 0);
}
if (ok) ok = (bgzf_write(fp, x, 32) >= 0);
if (ok) ok = (bgzf_write(fp, b->data, c->l_qname - c->l_extranul) >= 0);
if (ok) ok = (bgzf_write_small(fp, x, 32) >= 0);
if (ok) ok = (bgzf_write_small(fp, b->data, c->l_qname - c->l_extranul) >= 0);
if (c->n_cigar <= 0xffff) { // no long CIGAR; write normally
if (ok) ok = (bgzf_write(fp, b->data + c->l_qname, b->l_data - c->l_qname) >= 0);
if (ok) ok = (bgzf_write_small(fp, b->data + c->l_qname, b->l_data - c->l_qname) >= 0);
} else { // with long CIGAR, insert a fake CIGAR record and move the real CIGAR to the CG:B,I tag
uint8_t buf[8];
uint32_t cigar_st, cigar_en, cigar[2];
Expand All @@ -918,17 +909,16 @@ int bam_write1(BGZF *fp, const bam1_t *b)
cigar[1] = (uint32_t)cigreflen << 4 | BAM_CREF_SKIP;
u32_to_le(cigar[0], buf);
u32_to_le(cigar[1], buf + 4);
if (ok) ok = (bgzf_write(fp, buf, 8) >= 0); // write cigar: <read_length>S<ref_length>N
if (ok) ok = (bgzf_write(fp, &b->data[cigar_en], b->l_data - cigar_en) >= 0); // write data after CIGAR
if (ok) ok = (bgzf_write(fp, "CGBI", 4) >= 0); // write CG:B,I
if (ok) ok = (bgzf_write_small(fp, buf, 8) >= 0); // write cigar: <read_length>S<ref_length>N
if (ok) ok = (bgzf_write_small(fp, &b->data[cigar_en], b->l_data - cigar_en) >= 0); // write data after CIGAR
if (ok) ok = (bgzf_write_small(fp, "CGBI", 4) >= 0); // write CG:B,I
u32_to_le(c->n_cigar, buf);
if (ok) ok = (bgzf_write(fp, buf, 4) >= 0); // write the true CIGAR length
if (ok) ok = (bgzf_write(fp, &b->data[cigar_st], c->n_cigar * 4) >= 0); // write the real CIGAR
if (ok) ok = (bgzf_write_small(fp, buf, 4) >= 0); // write the true CIGAR length
if (ok) ok = (bgzf_write_small(fp, &b->data[cigar_st], c->n_cigar * 4) >= 0); // write the real CIGAR
}
if (fp->is_be) swap_data(c, b->l_data, b->data, 0);
return ok? 4 + block_len : -1;
}
#undef bgzf_write

/*
* Write a BAM file and append to the in-memory index simultaneously.
Expand Down

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