2.15.0

This release includes new features and bug fixes. There are no known compatibility issues with previous releases. Users are recommended to upgrade, particularly if they require support for very long reads.

Support for long CIGARs:

htsjdk can now read and write bam files with long CIGAR strings. This allows very long reads that have complicated alignments to be represented in bam. Previously the limit was 65535 CIGAR elements per read which is insufficient for new long read sequencing technology. See for more details about the internal representation samtools/hts-specs#227. (#1086)

Improvements to SortingCollection

SortingCollection now uses java parallel for some speedup and does a better job estimating available memory availability. #1111, #1109

Other updates:
adf428f Make BlockCompressedFilePointerUtil.makeFilePointer public (#1116)
1bbd3cf Fix typos and add defaults to javadoc in Defaults (#1114)
8b63854 renaming IoUtilTest and minor refactoring (#990)
1aaba3d reduce garbage creation when writing VCF (#1110)
73bf89c Add support for long reference sequences (#980)
447f82e fix compilation error caused by typo (#1106)
e266acc improve documentation in SAMRecord (#1036)
a5be9f2 upgrade jacoco version to 0.8.0 (#1102)
4245d9d FTP tests moved to separate test target (#1104)
673eaf7 Adding check on validator on VCFHeadLineCount (#1093)
ae57c10 prevent SamLocusIterator.accumulateIndels printing unecessary newlines (#1095)
7a38277 throw a clear exception if writing vcf without a header set #1008 (#1090)
d482e78 aesthetic changes only (#1087)