0.8.0

BREAKING

• cljam.io.tabix is rewritten. #180
• cljam.io.bam-index.writer/pos->lidx-offset is moved to cljam.io.util.bin/pos->lidx-offset. #180
• cljam.io.sam.util/reg->bin is moved to cljam.io.util.bin/reg->bin. Also, a coordinate system of its argument is changed from 0-based half-open to 1-based fully-closed. #190

Added

• Add support for random reading of vcf file. #180
• Add support for CSI reader. #182
• Add support for random reading of a bcf file. #187
• Add support for generating CSI file from bgzip compressed VCF. #190
• Add lint actions. #195
• Add support for generating CSI file from BCF. #196
• Add support cloning VCF/BCF. #200
• Create an index file while writing a sorted BAM file. #197

Changed

• Migrate CI to GitHub Actions. #181
• Detect the latest build number of OpenJDK EA. #183
• Improve performance for reading string from BCF. #186
• Improvement for pileup memory usage. #188
• Replace memoizing cache for parsed CIGARs with core.memoize's LU cache. #189
• Apply cljfmt. #191
• Fix warnings and errors reported by clj-kondo. #192
• Update actions/checkout to v2. #193
• Run lein check on CI. #199
• Refactor cljam.io.util.bin. #201
• Refactor cljam.io.csi. #202

Fixed

• Fix a bug in reading bgzipped VCF files. #184
• Fix float reader for specific environments such as IcedTea. #185
• Fix reading chrs when chrs in index file and chr are not equal. #194
• Add base_sha option to clj-lint-action. #198