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Prevent redundant copies of hash keys in string pools #1982

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Prevent redundant copies of hash keys in string pools #1982

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32 changes: 19 additions & 13 deletions cram/cram_encode.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3197,18 +3197,21 @@ static sam_hrec_rg_t *cram_encode_aux(cram_fd *fd, bam_seq_t *b,
// And and increment TD hash entry
BLOCK_APPEND_CHAR(td_b, 0);

// Duplicate key as BLOCK_DATA() can be realloced to a new pointer.
key = string_ndup(c->comp_hdr->TD_keys,
(char *)BLOCK_DATA(td_b) + TD_blk_size,
BLOCK_SIZE(td_b) - TD_blk_size);
if (!key)
goto block_err;
key = (char *)BLOCK_DATA(td_b) + TD_blk_size;
k = kh_put(m_s2i, c->comp_hdr->TD_hash, key, &new);
if (new < 0) {
goto err;
} else if (new == 0) {
} else if (new == 0) { // Seen this one before
BLOCK_SIZE(td_b) = TD_blk_size;
} else {
// New entry. As BLOCK_DATA() can be realloced, copy the
// key into a string pool and use this as the key in the hash table.
char *pooled_key = string_ndup(c->comp_hdr->TD_keys,
(char *)BLOCK_DATA(td_b) + TD_blk_size,
BLOCK_SIZE(td_b) - TD_blk_size);
if (!pooled_key)
goto block_err;
kh_key(c->comp_hdr->TD_hash, k) = pooled_key;
kh_val(c->comp_hdr->TD_hash, k) = c->comp_hdr->nTL;
c->comp_hdr->nTL++;
}
Expand Down Expand Up @@ -3791,17 +3794,20 @@ static int process_one_read(cram_fd *fd, cram_container *c,
//fprintf(stderr, "Checking %"PRId64"/%.*s\t", rnum,
// cr->name_len, DSTRING_STR(s->name_ds)+cr->name);
if (cr->flags & BAM_FPAIRED) {
char *key = string_ndup(s->pair_keys, bam_name(b), bam_name_len(b));
if (!key)
return -1;

k = kh_put(m_s2i, s->pair[sec], key, &new);
k = kh_put(m_s2i, s->pair[sec], bam_name(b), &new);
if (-1 == new)
return -1;
else if (new > 0)
else if (new > 0) {
// bam_name(b) is likely to change, so copy it to a string pool
// and use that for the hash table key.
char *key = string_ndup(s->pair_keys, bam_name(b), bam_name_len(b));
if (!key)
return -1;
kh_key(s->pair[sec], k) = key;
kh_val(s->pair[sec], k) = rnum
| ((unsigned)((cr->flags & BAM_FREAD1)!=0)<<30)
| ((unsigned)((cr->flags & BAM_FREAD2)!=0)<<31);
}
} else {
new = 1;
k = 0; // Prevents false-positive warning from gcc -Og
Expand Down