split async samtools and tribble options #529
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| @@ -19,9 +19,18 @@ | |||
| /** Should MD5 files be created when writing out SAM and BAM files? Default = false. */ | |||
| public static final boolean CREATE_MD5; | |||
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| /** Should asynchronous I/O be used when writing out SAM and BAM files (one thread per file). Default = false. */ | |||
| /** Should asynchronous I/O be used when writing out SAM, BAM, FASTQ files (one thread per file). Default = false. */ | |||
| @Deprecated | |||
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I don't think this should be deprecated. The semantics of this option are actually unchanged -- differences only arise if you opt-in to use of one of the two new options below.
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Also, you should mention explicitly in the docs for both this option and the others below that this option takes precedence over the other two.
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Review complete -- back to @akiezun |
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back to @droazen |
| @@ -19,9 +22,26 @@ | |||
| /** Should MD5 files be created when writing out SAM and BAM files? Default = false. */ | |||
| public static final boolean CREATE_MD5; | |||
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| /** Should asynchronous I/O be used when writing out SAM and BAM files (one thread per file). Default = false. */ | |||
| /** Should asynchronous I/O be used where supported in tribble/samtools/etc. (one thread per file). | |||
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"in tribble/samtools/etc." -> "throughout all of htsjdk"
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Second-pass review complete -- back to @akiezun. Merge after addressing comments. |
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split async samtools and tribble options
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Description
This PR takes over from #528 and splits
USE_ASYNC_IOinto 2 options,USE_ASYNC_IO_FOR_SAMTOOLSandUSE_ASYNC_IO_FOR_TRIBBLEbecause clients like GATK want more fine grained controls and also the performance characteristics of samtools vs tribble are very different (see #528) for examples and timings.@droazen can you review? @yfarjoun FYI