2.16.1

This is a relatively small release which includes bug fixes and some new features. Users should upgrade from 2.16.0.

New Feature: Write VCF to Paths

You can now write vcfs to NIO Paths including gcs Paths.
4902ee9 VCFWriter accepts Path (#1134)

Compatibility:

This release is binary compatible with 2.16.0. There are some new overloads of methods which may require minor source changes where they were previously being called with untyped nulls.

Deprecations

Some poorly named methods are now deprecated.
e0bf651 locatable all the things (#1159)
c4dbf4a fixing spelling Indeces -> Indices (#1157)

Other updates and bugfixes:

fb36a36 adding back deleted method(#1178)
e37d8de extending use of IOUtil.toPath() (#967)
85580fc restore no-args VariantContextWriterBuilder.build() (#1177)
16704e6 Use quality header and SAMTag.CO in FastqEncoder (#912)
e637281 Expose VCFCodec version and header fields. (#1176)
57442bb Fix a bug where invalid bytes in BufferedInputStream's buffer were being accessed. (#1175)
5168c79 Fix CRAM container offset calculation (#1167)
e6d5c29 fix an copy-paste error in VCFHeader (#1160)
8767e64 adding position to SAMRecord.toString() (#1158)
c4912e9 update to gradle 4.8 (#1154)
c380053 Fixes for CachingBAMFileIndex (#1156, #1127)
38a24d5 Additional unit tests for IOUtil (#1149)