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Zero the external array buffer before it is written to the file #335

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Zero the external array buffer before it is written to the file #335

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12 changes: 12 additions & 0 deletions api/hdf5_impl/hdf5ExternalArray.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@

#include "hdf5ExternalArray.h"
#include <cassert>
#include <cstring>
#include <iostream>

using namespace hal;
Expand All @@ -30,6 +31,17 @@ void Hdf5ExternalArray::initBuf() {
_bufEnd = _bufSize - 1;
delete[] _buf;
_buf = new char[_bufSize * _dataSize];
// Zero it. Not every byte of the buffer is written before it is flushed -- the
// bottom segment "length" field never is, since lengths are derived from the next
// segment's start -- and whatever the allocator handed back would otherwise be
// serialised into the file, leaving two runs that produced the same alignment
// differing byte for byte.
//
// This has to cover load() as well as create(): a file opened for modification
// reaches its arrays through Hdf5Genome::read(), which loads them, and segments
// are then written through those buffers. Zeroing only on create() leaves
// uninitialised bytes in the merged output of halAppendSubtree.
memset(_buf, 0, _bufSize * _dataSize);
}

// Create a new dataset in specifed location
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