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Fix multi-threading bug that causes incorrect results#106
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jmarshall wants to merge 1 commit intogenome:masterfrom
Open
Fix multi-threading bug that causes incorrect results#106jmarshall wants to merge 1 commit intogenome:masterfrom
jmarshall wants to merge 1 commit intogenome:masterfrom
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Having `m_filteredReads.push_back(m_rawreads[i])` in a loop that is parallel for `i` meant that entries could be pushed onto `m_filteredReads` in arbitrary order when multiple threads are used. Instead store pointers in a fixed-size array in the parallel loop, and squash them sequentially into `m_filteredReads` afterwards. Fixes a bug whereby incorrect output was produced when multiple threads were used (differences observed beyond six threads).
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We have observed that, for a fraction of the events detected in our data files, Pindel output varies with the number of threads Pindel uses. Specifically the per-sample per-strand counts are incorrect — 350+51 = 401 = 277+124, i.e., the total number of supporting reads is unchanged, but some of the reads have been assigned to the wrong strand:
Output was unchanged for low threading settings, but starts to differ at T=7 and by T=16 is dramatically incorrect.
This is fixed (and the output no longer varies with the number of threads used) by correcting
ReadBuffer::flush()to maintain the order ofm_rawreads[]entries when they are copied intom_filteredReads[]regardless of threading indeterminacy.I suspect this patch may also fix or affect #26, which appears to be a similar problem.