3.0.0

Htsjdk 3.0.0: Revenge of the Simple Allele

This is the first htsjdk with a major version increase in a long time. We bumped it to indicate there are some breaking changes that will potentially require downstream code changes. Notably, Allele became an interface instead of a concrete class. SimpleAllele may be used as a replacement if you have classes which previously subclassed allele.

New Plugin Infrastructure:
6a60de7 Move API marker annotations into new annotation package. (#1558)
7ac95d5 Plugin framework and interfaces for versioned file format codecs (#1525)
d40fe54 Beta implementation of Bundles. (#1546)

CRAM
489c419 Support CRAM reference regions. (#1605)
22aec67 Fix decoding of CRAM Scores read feature during normalization. (#1592)
6507249 Make the CRAM MD5 failure message more user friendly. (#1607)
b5af659 Fix restoration of read base feature code. #1379 (#1590)
e63c34a Ignore TC, TN on CRAM read (#1578)

BAM/SAM
1449dec Support loading of CSI from URLs/streams. #1507 (#1595)
a38c78d Add an option to SAMFileWriter to disable checking of ordering of rec… (#1599)
51aa6ed Validate that SAM header tag keys are exactly 2 characters long (#1561)
fbd9e96 Deprecate OTHER as a PL value (#1552)
d5f7e10 Adding PL Tag 'DNBSEQ' as the Platform/Technology for BGI/MGI (#1547)

Misc Improvements
f461401 Silence AsciiLineReader warning when creating a FASTA sequence index (#1559)
8f82871 Update explain samflags script to python3 (#1585)
4ba4c06 Update to new version of the snappy library which will work with M1 macs (#1580)
e927064 add predicate to GFF3Codec to give a chance to filter out some unused attributes (#1575)
c647764 Some long reads tests using PacBio data. (#1564)
57c3f03 remove hardcoded .idx (#1568)
a94a325 Add file extension to missing index error message #1512 (#1567)
74b827b Improve error message in IntervalTree (#1545)
7719274 Htsget POST request support (#1529)

VCF:
aac46ee Added GVCF mode for VariantContext type determination (#1544)
d72d73b Add context to exception when the vcf file is invalid #1565 (#1566)
8466c82 Respect genotype filtering when calculating AC/AN/AF (#1554)

User API:
a4f1f04 Allow fluent chaining setters for SAMSequenceRecord (#1563)
08628f5 Rename ByteArrayAlelle to SimpleAllele and make it public (#1576)
0044297 Convert Allele to an Interface(#1454)

Infrastructure:
70e4259 Remove unnecessary println in test (#1602)
c0b61a2 Upgrade to samtools 1.14. (#1583)
b2b31ab Adding Github actions as an alternative to travis. (#1572)
8e8ae5c Validating the codecov script when downloading. (#1549)