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modified: src/main/java/picard/analysis/CollectInsertSizeMetrics.java
modified: src/main/java/picard/analysis/CollectGcBiasMetrics.java modified: src/main/java/picard/analysis/CollectInsertSizeMetrics.java
…e from walker and executing method accpetRead Created Semaphore to limit number of in-memory objects Tested. Works.
Deleted debug output (measuring time), wrote comments
kamyshova
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Apr 16, 2017
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kamyshova
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kamyshova
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Исправьте замечания + поработайте с sonar. И попробуйте распараллелить по программам.
| if (walker == null || tmpRecord.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) { | ||
| ref = null; | ||
| } else { | ||
| ref = walker.get(tmpRecord.getReferenceIndex()); |
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Вы точно уверены, что этот код синхронизирован? Потому как walker не синхронизирован.
| ExecutorService acceptReadService = Executors.newSingleThreadExecutor(); | ||
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| //Limit for tasks into services' queues | ||
| Semaphore semaphore = new Semaphore(SEMAPHORE_PERMITS); |
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Лучше использовать BlockingQueue с размером в ThreadPool.
| try { | ||
| refReadService.awaitTermination(1, TimeUnit.DAYS); | ||
| } catch (InterruptedException e) { | ||
| e.printStackTrace(); |
| public void run() { | ||
| for (Pair<SAMRecord, ReferenceSequence> pair : pairs) { | ||
| for (final SinglePassSamProgram program : programs) { | ||
| program.acceptRead(pair.getKey(), pair.getValue()); |
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Нельзя, чтобы параллельно на одной программе обрабатывалось несколько рекордов.
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Description
Used two SingleThreadExecutors for parallel computing in makeItSo
Didn't use JMH yet
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