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Only realloc(pac,...) if it needs to be made larger 

Similarly to the realloc(pac,...) within add1(), only bother to call
realloc() if appending the reverse complemented sequence requires more
space than is currently in the pac/m_pac buffer.

Avoids realloc(pac,0) (and a "Failed to allocate 0 bytes at bntseq.c"
message from wrap_realloc()) in the corner case of an empty reference
FASTA file.  Fixes #54.
This commit is contained in:
John Marshall 2017-05-10 19:47:12 +01:00
parent beff2e27f8
commit 1972a97813
1 changed files with 3 additions and 3 deletions
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6
bntseq.c
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@ -299,9 +299,9 @@ int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only)
// read sequences
while (kseq_read(seq) >= 0) pac = add1(seq, bns, pac, &m_pac, &m_seqs, &m_holes, &q);
if (!for_only) { // add the reverse complemented sequence
m_pac = (bns->l_pac * 2 + 3) / 4 * 4;
pac = realloc(pac, m_pac/4);
memset(pac + (bns->l_pac+3)/4, 0, (m_pac - (bns->l_pac+3)/4*4) / 4);
int64_t ll_pac = (bns->l_pac * 2 + 3) / 4 * 4;
if (ll_pac > m_pac) pac = realloc(pac, ll_pac/4);
memset(pac + (bns->l_pac+3)/4, 0, (ll_pac - (bns->l_pac+3)/4*4) / 4);
for (l = bns->l_pac - 1; l >= 0; --l, ++bns->l_pac)
_set_pac(pac, bns->l_pac, 3-_get_pac(pac, l));
}