A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.
All credits to Broad Institute [ORIGINAL REPO]
Main goal was to redesign Estimated Library Complexity from sequential to concurrent implementation, also SortingCollection was rewritten in concurrent & thread-safe way.
There are 3 different concurrent implementation, the best and the most performance one [STREAM], and the two least code-clean and may be less performance.
Also [EXECUTOR] version contains all Predicates, abstract collection and etc, which are used in all Concurrent implementations.
P.S. All help and support classes and predicates were grouped in [EXECUTOR] intentionally.
Estimated Library Complexity [ORIGINAL]
Custom Estimated Library Complexity [STREAM | POOL | EXECUTOR]
Sorting Collection [ORIGINAL]
Custom Sorting Collection [CUSTOM]
Abstraction wrapper over PeekableIterator, used to read and filter sorted files in async mode. [QueueProducer]
| Heap Size | Bam File Size | JDK | Processor |
|---|---|---|---|
| 256mb | 464mb | 1.8.0_121 (64bit) | i3-4030u 1x2x2 |
| Implementation Name | Avegange Time (ms) | Amount of iteratins | MaxPairsInMemoty |
|---|---|---|---|
| Default | 55541.009 | 5 | 169196 |
| ConcurrentExecutorELC | 37775.565 | 5 | 169196 |
| ConcurrentPoolELC | 39255.594 | 5 | 169196 |
| ConcurrentStreamedELC | 40355.021 | 5 | 169196 |
- The best custom implementation is 47% faster.
| Heap Size | Bam File Size | JDK | Processor |
|---|---|---|---|
| 4gb | 16.9gb | 1.8.0_121 (64bit) | i3-4030u 1x2x2 |
| Implementation Name | Avegange Time (ms) | Amount of iteratins |
|---|---|---|
| Default | 1972577.978 | 5 |
| ConcurrentExecutorELC | 1253195.879 | 5 |
- Custom impelemntation is 57.4% faster.
- To build a fully-packaged, runnable Picard jar with all dependencies included, run:
./gradlew shadowJar
- The resulting jar will be in
build/libs. To run it, the command is:
java -jar build/libs/picard.jar
or
java -jar build/libs/picard-<VERSION>-all.jar
- To build a jar containing only Picard classes (without its dependencies), run:
./gradlew jar
- To clean the build directory, run:
./gradlew clean