0.8.5

Changed

• Use aset instead of aset-* for performance #286
• Misc performance tuning for cljam.algo.depth #287
• Disable :missing-docstring linter for test code #288
• Use ByteBuffer wrapper instead of LSB protocol #290
• Rewrite TwoBitWriter using FileChannel and ByteBuffer #291
• Replace remaining LSB protocol implementations with ordinary functions #293
• Remove nth's linear search overhead in BCF reader #294

Fixed

• Fix/apply lint #269
• Fix/vcf float case insensitive #272
• Fix/additional coding style #279
• Fix/shadowing var #281
• Fix/add doc string #282
• Remove extra parens around static field references #300
• Update dependencies #310

Added

• Add function for unphasing genotypes #275
• Support explicit first phasing indicator for VCF genotypes #276
• Add validator for writing vcf. #277
• Add validator for writing sam. #278
• Implementing rANS4x8 decoder toward CRAM support #297
• Add CRAM reader (alpha) #302
• Misc performance improvements for CRAM reader #304
• Index-based random access for CRAM reader #306
• Support reading CRAM files with embedded references #307
• Automatic read name generation for CRAM records #308
• Support for CRAM beta coding #309
• Support for reading alignments in specific region without CRAI index file #311

Full Changelog: 0.8.4...0.8.5

0.8.4

Changed

• Bump actions/checkout from 2.4.0 to 3 #254
• Bump actions/cache from 2.1.7 to 3 #255
• Bump codecov/codecov-action from 2.1.0 to 3 #256
• Bump actions/setup-java from 2 to 3 #257
• Bump xcoo/clj-lint-action from 1.1.10 to 1.1.11 #262

Fixed

• Fix error that occurs when encoding a value greater than 32767 with ‘B, S’ data type in encoding alignment in encoding alignment. #264
• Fix cljam.io.bam-test to work properly #266
• fix: overflowing qual value in vcf #268

Added

• Support CIGARs longer than 65535 operations #263
• Extend the supported data types in encoding alignment options #265

0.8.3

Changed

• Bump actions/checkout from 2.3.4 to 2.3.5. #248
• Bump actions/checkout from 2.3.5 to 2.4.0. #249
• Bump actions/cache from 2.1.6 to 2.1.7. #250

Fixed

• Avoid StackOverflowError while reading a VCF with many lines of meta. #252
• Use bgzip as default for writing .gz files. #253

0.8.2

Changed

• Bump xcoo/clj-lint-action from 1.1.9 to 1.1.10. #246

Fixed

• Fix error that occurs when querying intervals for missing chr. #247

0.8.1

Added

• Add support for fast interval finder. #209
• Add support for nclist. #211
• Add support for indexed? for vcf/bcf. #212

Changed

• Update the version of lint-action to read the clj-kondo config file. #203
• Introduce GitHub Dependabot to keep dependencies up to date. #204
• Bump codecov/codecov-action from v1.0.3 to v1.0.10. #205
• Bump codecov/codecov-action from v1.0.10 to v1.0.12. #207
• Bump codecov/codecov-action from v1.0.12 to v1.0.13. #208
• Bump xcoo/clj-lint-action from v1.1.6 to v1.1.7. #210
• Bump codecov/codecov-action from v1.0.13 to v1.0.14. #213
• Bump codecov/codecov-action from v1.0.14 to v1.0.15. #214
• Update java versions for testing. #215
• Bump codecov/codecov-action from v1.0.15 to v1.1.0. #216
• Bump codecov/codecov-action from v1.1.0 to v1.1.1. #217
• Bump codecov/codecov-action from v1.1.1 to v1.2.0. #218
• Bump codecov/codecov-action from v1.2.0 to v1.2.1. #219
• Bump actions/cache from v2 to v2.1.4. #220
• Bump codecov/codecov-action from v1.2.1 to v1.2.2. #221
• Bump codecov/codecov-action from v1.2.2 to v1.3.1. #222
• Bump codecov/codecov-action from v1.3.1 to v1.3.2. #225
• Update actions/setup-java to v2. #226
• Bump actions/cache from v2.1.4 to v2.1.5. #227
• Bump codecov/codecov-action from v1.3.2 to v1.4.0. #229
• Bump codecov/codecov-action from v1.4.0 to v1.4.1. #230
• Bump xcoo/clj-lint-action from v1.1.7 to v1.1.8. #231
• Bump codecov/codecov-action from v1.4.1 to v1.5.0. #232
• Bump actions/checkout from 2 to 2.3.4. #233
• Bump actions/cache from 2.1.5 to 2.1.6. #234
• Bump xcoo/clj-lint-action from 1.1.8 to 1.1.9. #235
• Add explanation to info exception. #236
• Bump codecov/codecov-action from 1.5.0 to 1.5.2. #237
• Fix bam encoder/decoder to convert sam to bam. #239
• Fix parser generation not to interpret unnecessary data when calculat…. #241
• Bump codecov/codecov-action from 1.5.2 to 2.0.1. #242
• Bump codecov/codecov-action from 2.0.1 to 2.0.2. #243
• Bump codecov/codecov-action from 2.0.2 to 2.0.3. #244
• Bump codecov/codecov-action from 2.0.3 to 2.1.0. #245

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

0.7.4

Fixed

• Fix creating temp directory to support multiple users. #178
• Avoid an ArityException on creating an index for BAM files without alignments. #179

0.7.3

Added

• Add content-based file type detection. #171
• Add support for random reading of bgzipped FASTA files. #174

Fixed

• Fix I/O of variants with empty info/individual fields. #167
• Fix bugs in BCF I/O. #168
• Ignore undeclared keys in INFO and FORMAT when writing BCF files. #169
• Provide a default file format version for BCF. #170
• Fix nonintentional paths. #172
• Fix decoding of long CIGAR ops in BAM. #173
• Fix reflection warnings. #175
• Fix minor typos. #176
• Fix grammar. #177

0.7.2

See changelog

0.7.1

See change log