2.11.0

This release includes major bug fixes to cram and indexing code, as well as other bug fixes and improvements. Most users should update.

Several long standing bugs which caused creation of incorrect indexes on tribble files have been fixed. This could cause queries to return incorrect results. One of the issues only manifested when a VCF header was large, which made it apparent with hg38 where had been much rarer previously. It's recommended that anyone creating indexes with htsjdk should upgrade. The fix necessitated changes to the indexing code which may break tribble codecs that relied on the old behavior. See #906 for more details as well updates to the codec contract that make the new behavior clear. In particular codecs that have internal buffering readers will have problems. If you are a codec author it's recommended that you carefully test these indexing changes with your codec before upgrading.

SamFileValidator now performs more complete validation which may cause files that previously passed validation to now fail validation.

Deprecated SAMTools and SAMRecordUtils these will be removed in a future release.

Complete change list:
2b5736f additional tests and a few misc improvements (#884)
86a408c close stream in IndexFactory #297 (#964)
1c44869 Fix bugs in IndexFactory and BinningIndexBuilder. #393 #943 (#906)
03e8eaa Broke out the static variables for VCF suffixes (#960)
3ae056c Updated javadocs for the query method (#954)
81ac548 Should write to /dev/stdout as a special case. (#933)
3ad7948 deprecate SAMTools.java (#937)
69f31b5 Increase test coverage for Cigar classes (#939)
1969eb8 Replace bad .fai test file and create one new CRAMComplianceTest data provider. (#940)
d0f0ba1 Add ability to redirect log to an alternate print Stream #941 (#942)
cfbbe4b fix for ambiguity and lc match/mismatch bases in CRAM (#889)
624a3bf Add missing HtsjdkTest marker to test classes (#936)
8d207ae Updates to readme about documentation, communication & license. (#916)
1cd23da Make stream seek error message informative (#927)
7d31bc2 Adding the gitter badge (#915)
c20e0ed Add more checks to SamFileValidator #899 (#907)
8f89e27 Sort and group order not updated when using setAttribute. (#905)
04fd13e more care checking terminator blocks while closing BlockCompressedOutputStream. (#901)
cc538e2 Typekpb patch 1 (replacing #725) (#883)
9f1f191 Standardizes mate info computation in SAMRecordSetBuilder. (#692)
6383b25 Fixed flipped sign when comparing read paired flags #256 (#897)
4626fe6 updating artifactory link to point to new artifactory (#892)
9b84fe8 Cleaned up SAMUtils (mostly cosmetic) (#888)
112758b Added test using setReadString() #297 (#893)
7e79bba use Locatable interface (#887)
9e0199a Fix SAMRecord.getReadLength() so it does not throw an exception if null bases #297 (#893)