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@lbergelson lbergelson released this 30 Aug 17:28
· 572 commits to master since this release
2.6.1
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lbergelson Louis Bergelson
GPG key ID: CC068B4BECC94A5F
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c3d5a88

Minor release with bug fixes and new methods.

This release while not technically source compatible with 2.6.0 should not require any changes by the vast majority of users.

Added new checks to prevent reading a CRAM file with the wrong reference sequence. It is recommended that CRAM users upgrade since accidentally reading a CRAM file with a different reference than it was created with results in reading incorrect bases.

Deprecated TribbleIndexedFeatureReader.isGZIPPath, use TribbleIndexedFeatureReader.hasBlockCompressedExtension instead.

c3d5a88 added function to extract SA tag and return a list of supplementary alignments (#685)
275cfe0 Removed unused .bcf test files. (#691)
0d0da87 Throw on unrecognized CRAM encoding tag. (#593)
b81d036 Remove unreferenced test files. (#687)
0e17e07 Added a "RANDOM" duplicate scoring strategy. (#688)
a781afa Normalize CRAM reference bases and throw on MD5 validation failure.
c8202f2 Fix TribbleIndexedFeatureReader cannot read header from .bgz #653 (#672)
fba4637 FeatureCodec.getTabixFormat() to encapsulate tabix formatting (#669)
c872049 Add mention of test.single to README
ea80585 Fix self-suppression problem with exception handling in AbstractAsyncWriter

Thank you to all of our contributors!

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