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Fix buffer overflow in BAM output for long reads #54

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Fix buffer overflow in BAM output for long reads #54

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31 changes: 19 additions & 12 deletions src/ProcessReads.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -850,9 +850,21 @@ void MasterProcessor::writeBam(const std::string& ostr, int readNameLen, int rea
nlen += rname_original_len; // Add the original --mod-names back in if --mod-names-bam is specified
}

static char buf1[32768];
static char buf2[32768];
bam1_t b1;
const int lseq = (slen+1)>>1;
size_t tag_bytes = 0;
for (const auto& bam_tag : bam_tags) {
if (bam_tag.length() < 5) continue;
if (bam_tag[2] != ':' || bam_tag[4] != ':') continue;
if (bam_tag[3] == 'Z') {
tag_bytes += 3 + (bam_tag.length()+1-5);
} else if (bam_tag[3] == 'i') {
tag_bytes += 7;
}
}
const size_t data_capacity = static_cast<size_t>(nlen + lseq + qlen) + tag_bytes;
std::vector<uint8_t> buffer(data_capacity);

bam1_t b1{};
bam1_core_t core1;
core1.tid = -1;
core1.pos = -1;
Expand All @@ -871,11 +883,10 @@ void MasterProcessor::writeBam(const std::string& ostr, int readNameLen, int rea
core1.flag |= BAM_FPAIRED | BAM_FREAD2;
}
b1.core = std::move(core1);
uint8_t* buf = (uint8_t*)&buf1[0];
uint8_t* buf = buffer.data();
memcpy(buf, name, nlen);
int p = core1.l_qname;
// copy the sequence
int lseq = (slen+1)>>1;
uint8_t *seqp = (uint8_t *) (buf+p);
memset(seqp,0,lseq);
for (int i = 0; i < slen; ++i) {
Expand All @@ -888,24 +899,22 @@ void MasterProcessor::writeBam(const std::string& ostr, int readNameLen, int rea
}
p += qlen;
b1.l_data = p;
b1.m_data = core1.l_qname + ((core1.l_qseq+2)>>1) + core1.l_qseq;
b1.m_data = static_cast<int>(buffer.size());
b1.data = buf; // structure: qname-cigar-seq-qual-aux
for (auto& bam_tag: bam_tags) { // XX:X:XXXX
if (bam_tag.length() < 5) continue;
b1.data[b1.l_data] = bam_tag[0];
b1.data[b1.l_data+1] = bam_tag[1];
if (bam_tag[2] != ':') continue;
if (bam_tag[4] != ':') continue;
b1.data[b1.l_data] = bam_tag[0];
b1.data[b1.l_data+1] = bam_tag[1];
b1.data[b1.l_data+2] = bam_tag[3];
if (bam_tag[3] == 'Z') { // The value of our BAM tag is a string
memcpy(b1.data + b1.l_data + 3, bam_tag.c_str()+5, bam_tag.length()+1-5);
b1.l_data += 3+bam_tag.length()+1-5;
b1.m_data += 3+bam_tag.length()+1-5;
} else if (bam_tag[3] == 'i') { // The value of our BAM tag is an integer
int val = std::atoi(bam_tag.c_str()+5);
memcpy(b1.data + b1.l_data + 3, &val, 4);
b1.l_data += 7;
b1.m_data += 7;
}
}
int ret = 0;
Expand Down Expand Up @@ -1324,5 +1333,3 @@ FastqSequenceReader::FastqSequenceReader(FastqSequenceReader&& o) :
o.seq.resize(nfiles, nullptr);
o.state = false;
}