Package htsjdk.beta.plugin.reads
Class ReadsEncoderOptions
java.lang.Object
htsjdk.beta.plugin.reads.ReadsEncoderOptions
- All Implemented Interfaces:
HtsEncoderOptions
General reads encoder options.
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionGet theBAMEncoderOptions
for these ReadsEncoderOptions.Get theCRAMEncoderOptions
for this ReadsEncoderOptions.boolean
Get the preSorted setting for these options.setBAMEncoderOptions
(BAMEncoderOptions bamEncoderOptions) Set theBAMEncoderOptions
for these ReadsEncoderOptions.setCRAMEncoderOptions
(CRAMEncoderOptions cramEncoderOptions) Set theCRAMEncoderOptions
for these ReadsEncoderOptions.setPreSorted
(boolean preSorted) Set the preSorted setting for these options.
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Constructor Details
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ReadsEncoderOptions
public ReadsEncoderOptions()
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Method Details
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isPreSorted
public boolean isPreSorted()Get the preSorted setting for these options. Default value is false. If isPresorted is false, output will be sorted as needed on write.- Returns:
- true if preSorted is true, otherwise false
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setPreSorted
Set the preSorted setting for these options. Default value is false. If preSorted is false, output will be sorted as needed on write.- Parameters:
preSorted
- the preSorted state for these options- Returns:
- updated ReadsEncoderOptions
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getBAMEncoderOptions
Get theBAMEncoderOptions
for these ReadsEncoderOptions. Defaults to defaultBAMEncoderOptions
.- Returns:
- the
BAMEncoderOptions
for these ReadsEncoderOptions
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setBAMEncoderOptions
Set theBAMEncoderOptions
for these ReadsEncoderOptions. Defaults values are defaultBAMEncoderOptions
.- Parameters:
bamEncoderOptions
-BAMEncoderOptions
to use for these ReadsEncoderOptions- Returns:
- updated ReadsEncoderOptions
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getCRAMEncoderOptions
Get theCRAMEncoderOptions
for this ReadsEncoderOptions. Default values are defaultCRAMEncoderOptions
.- Returns:
- the
CRAMEncoderOptions
for this ReadsEncoderOptions
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setCRAMEncoderOptions
Set theCRAMEncoderOptions
for these ReadsEncoderOptions. Defaults to defaultCRAMEncoderOptions
.- Parameters:
cramEncoderOptions
- theCRAMEncoderOptions
for these ReadsEncoderOptions- Returns:
- updated ReadsEncoderOptions
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