2.14.2

This release includes several important bug fixes. This release is backwards compatible with 2.14.1.

Known Regression:

This release introduced a regression (#1083) that prevents opening named pipes with SamReaderFactory.
Prefer 2.14.3 over this version.

Important fixes:

A longstanding issue that could cause reading block compressed vc.gz files to be truncated is fixed.
The issue was caused by a known bug in the java GZipInputStream implementation that make inappropriate use of the InputStream.available() method to detect end of stream.
The work-around was to implement available() on SeekableStream
See https://bugs.java.com/bugdatabase/view_bug.do?bug_id=7036144# for more information (and maybe prod the java team to fix this one...)

Fixed shutdown hooks that automatically delete Path to use a single shutdown hook instead of registering one for each path.

All changes:

5c8de55 Add DeleteOnExitPathHook to register java.nio.Path for deletion (#1037)
8b8d961 Implement SeekableStream.available #898 (#1077)
9d724c3 Performing CIGAR and sequence length only when both the read sequence and the CIGAR exists. (#1075)
88edbf3 Added filters to output of VariantContext.toString() #833 (#1074)
6e51261 move FastaSequenceIndexEntry to a separate file and make it public #1072