Upgrade to htsjdk 2.19.0 #77
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cmnbroad
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Jan 16, 2019
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Sorry @tomwhite - we're overhauling refactoring all the cram code in htsjdk. Well try to audit the disq usages as we do this going forward so we can get out a little in front of these.
LGTM once htsjdk is released and tests pass.
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Thanks @cmnbroad. It looks like htsjdk 2.18.2 does not have this change, so this PR is not needed (for now). |
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I didn't include the most recent several commits in htsjdk 2.18.2 because they introduced new issues like this and I wanted to get something out soon before dealing with that. We'll have a 2.19.0 pretty soon which includes those changes. |
…ry that affects CramSource in Disq. See the note about incompatible CRAM changes at https://github.com/samtools/htsjdk/releases/tag/2.17.0. This commit uses the new CRAIEntry API introduced in samtools/htsjdk#1256
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lbergelson
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Mar 13, 2019
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The changes to CRAM have introduced an incompatible change to CRAIEntry that affects CramSource in Disq. See the note about incompatible CRAM changes
at https://github.com/samtools/htsjdk/releases/tag/2.17.0.
This commit uses the new CRAIEntry API introduced in samtools/htsjdk#1256
Note: the change has not been released yet (so this PR will fail to compile), but a new htsjdk release is imminent, so the Disq 0.2.0 release should wait for it.