2.18.2

This is a small release which includes bug fixes and some new methods and performance improvements.

Compatibility notes:

This is compatible with 2.18.1 with the exception of the unstable htsjdk.samtools.cram package which continues to undergo major changes.

Disallowed Contig Names:

The following characters have been disallowed from being included in contig names: \ , "'`` () <> [] {} (#1238)

These are being disallowed in future versions of the SAM spec because they can introduce parsing ambiguities. We've chosen to disallow them in all versions of files read or produced by htsjdk going forward which is stricter than the spec. A scan of a large number of references found that they were used in only a tiny fraction of references. We believe this shouldn't cause users problems since these characters do not appear in common references, if we're wrong and this change causes you problems please get in touch and let us know.

Deprecations:

The classes in the htsjdk.samtools.apps package are deprecated and will be removed in the future.

Complete Change list

68d9fdb Fix to ensure that SeekableStream#available() never returns a negative value. (#1255)
5a0ab68 Fix nitpick in IntervalKeepPairFilterTest (#1254)
2c97cce IntervalKeepPairFilter now filters out single ended reads (#1252)
2737292 Deprecated htsjdk.samtools.apps package. (#1250)
0bf5ff6 Add getters to VariantContextBuilder (#1247)
a4b7da8 resolving some nitpicks from pr #1245 (#1246)
2473407 Added ability to get a VariantContexts from an InputStream (#1245)
4a7cb03 Adding some sanity checking to IntervalList reading. (#1230)
28dde96 Add support for reading and writing splitting BAM index files. (#1138)
37f0789 HttpUtils: set Method to HEAD for HttpUtils.getHeaders (#1191)
fb2f42c Add finals for issues raised in review of PR 1091. (#1240)
8cc1e37 Disallowing bad characters in SamRecord names (#1238)
6ac7a60 Change CRAM validation error reporting granularity from container to record (#1091)
1126e5c CRAM: Refactor Block hierarchy (#1231)
d2360ff Replaced several for-each loops in VariantContext.Make() based on HaplotypeCaller profiling (#1234)