Fix up adapter clipping tags after an adapter is selected #1020
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jacarey
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danxmoran
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Dec 8, 2017
| @@ -66,6 +72,9 @@ | |||
| private int numAdaptersSeen = 0; | |||
| private final CollectionUtil.DefaultingMap<AdapterPair, Integer> seenCounts = new CollectionUtil.DefaultingMap<AdapterPair, Integer>(0); | |||
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| //Store all the sam records we have seen prior to choosing and adapter so that we can go back and fix the ones | |||
| preAdapterPrunedRecords.get(ret).add(read1); | ||
| preAdapterPrunedRecords.get(ret).add(read2); | ||
| tallyFoundAdapter(ret); | ||
| } |
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Is it worth pulling this block into a separate method, to avoid the duplication?
| //remove all the reads for the selected adapters | ||
| Arrays.stream(adapters.get()).forEach(adapter -> preAdapterPrunedRecords.remove(adapter)); | ||
| //anything left is marked with the incorrect adapter and needs its XT tag removed | ||
| (preAdapterPrunedRecords.values()).forEach(readList -> readList.parallelStream().forEach(read -> { |
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Unneeded parens around preAdapterPrunedRecords.values()?
danxmoran
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Dec 8, 2017
| import java.util.Map; | ||
| import java.util.Objects; |
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In a multi-threaded environment there is a chance that basecalls to sam is not deterministic depending on which adapters it sees prior to adapter selection and which adapter it selects. This PR is mean to cache all read seen pre adapter selection and then go back and remove XT tags from reads that were clipped due to adapters other than the selected on being found.
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