Code

Misc CRAM cleanup#1253

Code

Merged

jmthibault79 merged 19 commits intomastersamtools/htsjdk:masterfrom jt_general_cramsamtools/htsjdk:jt_general_cramCopy head branch name to clipboardJan 17, 2019

+784-751

Commits

Commits on Jan 16, 2019

• rm IllegalAccessException

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• rm IllegalArgumentException

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• rm ExposedByteArrayOutputStream

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• rm IOException and EOFException

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• rm all other public throws

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• revert

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• misc cleanup HuffmanByteHelper

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• don't need this

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• more specific exception

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• Boundary implements Iterator<Container>

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• equivalent check

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• findBasesByMD5 now throws GaveUpException

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• Immutable GaveUpException

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• Can remove close b/c Closeable

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• more CRAMIterator cleanup

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• post rebase fix

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• Quash close() RuntimeIOException

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• rethrow IOExceptions as RuntimeIOExceptions

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• change 2 debug logs to infos

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