2.17.0

This is a small release that includes a number of bug fixes and minor enhancements.

Compatibility Notes:

This release is not backwards compatible with 2.16.1 due to changes in the cram code. We believe most users should be able to upgrade without issue.

htsjdk.samtools.cram package instability:

This release includes the beginning of work towards a rewrite of much of the cram code. This code is not structured like the rest of htsjdk and needs large compatibility breaking changes compatible changes in order to be brought in line with the rest of the codebase. We will be treating the code in this htsjdk.samtools.cram package as unstable and will not be providing deprecation warnings in releases before altering it like we try to do with most of the codebase.

We believe that there are few downstream users who directly call into that code and most users only interact with cram files through the CramFileWriter and CramFileReader which will not be changing. Please get in contact if you make extensive use of classes in the htsjdk.samtools.cram package and are concerned about these changes.

The end result will be better cram code that should run faster, have fewer bugs, and include more features that are not yet implemented in htsjdk.

JAXB removed

In order to improve htsjdk compatibility with java 9+ we have removed all uses of the javax.xml.bind package. This breaks the ability to marshal SAMFileHeader to XML, but since this was the only class that could be converted in this way we believe that there will be no users effected by this change.

Complete change list

c484241 MergeSamFiles accept SO:UNKNOWN (#1069)
f00a754 Remove JAXB (#1206)
44baddf Adding support for 0-length B arrays in SAM files to conform to 1.6 spec (#1194)
334800e Add the PS FORMAT VCF standard header field (#1200)
bbc674f BetaIntegerCodecTest and bugfixes (#1199)
37069a3 Unit Tests and fixes for a few classes in samtools.cram.io (#1198)
d504256 fix CRAMIterator when next() is called without hasNext() (#1193)
1971f4e Adding Allele constants for simple SV types(#1192)
23f3223 Add 6 CRAM compliance tests from htslib (#1185)
ff3db93 Bug fix: BinaryCodec should not fail when both reading and no bytes are requested. (#1188)
a7214ca Add a reset() method to ProgressLoggerInterface. (#1184)
49c70e5 fixing bug in SeekableHttpStream.read (#1182)
a762262 cleanup bam order checking code (#770)