chrovis/cljam issues and pull requests

#323 - Support for delta encoding of AP data series for sorted CRAM files

Pull Request - State: open - Opened by athos 29 days ago - 1 comment

#322 - Fine-grained partition of CRAM containers and slices

Pull Request - State: closed - Opened by athos about 1 month ago - 1 comment

#321 - Use XZ for LZMA compression in CRAM

Pull Request - State: closed - Opened by athos about 1 month ago - 2 comments

#320 - Block compression support for CRAM writer

Pull Request - State: closed - Opened by athos about 1 month ago - 1 comment

#319 - Refactor CRAM writer to organize encoding values into context maps

Pull Request - State: closed - Opened by athos 2 months ago - 2 comments

#318 - CRAM tag dictionary construction at preprocessing phase

Pull Request - State: closed - Opened by athos 2 months ago - 3 comments

#317 - Support for CRAM index generation

Pull Request - State: closed - Opened by athos 2 months ago - 2 comments

#316 - Problematic behaviors around BAM index generation

Issue - State: open - Opened by athos 3 months ago

#315 - SAM/BAM/CRAM readers don't support @CO header

Issue - State: open - Opened by athos 3 months ago
Labels: bug

#314 - Read/write invariance breaks with integer tags in BAM/CRAM

Issue - State: open - Opened by athos 3 months ago
Labels: bug

#313 - Add CRAM writer (alpha)

Pull Request - State: closed - Opened by athos 3 months ago - 1 comment

#311 - Support for reading alignments in specific region without CRAI index file

Pull Request - State: closed - Opened by athos 5 months ago - 1 comment

#310 - Update dependencies

Pull Request - State: closed - Opened by alumi 5 months ago - 2 comments
Labels: bug, dependencies

#309 - Support for CRAM beta coding

Pull Request - State: closed - Opened by athos 5 months ago - 1 comment

#308 - Automatic read name generation for CRAM records

Pull Request - State: closed - Opened by athos 5 months ago - 5 comments

#307 - Support reading CRAM files with embedded references

Pull Request - State: closed - Opened by athos 5 months ago - 4 comments

#306 - Index-based random access for CRAM reader

Pull Request - State: closed - Opened by athos 6 months ago - 2 comments

#305 - Suggestion on effective VCF file reading?

Issue - State: closed - Opened by dotinspace 6 months ago - 2 comments

#304 - Misc performance improvements for CRAM reader

Pull Request - State: closed - Opened by athos 6 months ago - 1 comment

#303 - Remove CLI functionality

Pull Request - State: closed - Opened by totakke 6 months ago - 1 comment

#302 - Add CRAM reader (alpha)

Pull Request - State: closed - Opened by athos 7 months ago - 1 comment

#301 - Test coverage fails sometimes on some environments

Issue - State: open - Opened by athos 7 months ago

#300 - Remove extra parens around static field references

Pull Request - State: closed - Opened by athos 8 months ago

#299 - Bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#298 - Bump actions/cache from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#297 - Implementing rANS4x8 decoder toward CRAM support

Pull Request - State: closed - Opened by athos 9 months ago - 3 comments

#296 - Remove `-Xbootlasspath/a` option of the cljam executable

Pull Request - State: closed - Opened by alumi 10 months ago - 2 comments
Labels: bug

#295 - `dict` command after cljam 0.8.2 fails

Issue - State: closed - Opened by totakke 10 months ago - 4 comments
Labels: bug

#294 - Remove nth's linear search overhead in BCF reader

Pull Request - State: closed - Opened by athos 10 months ago - 1 comment

#293 - Replace remaining LSB protocol implementations with ordinary functions

Pull Request - State: closed - Opened by athos 10 months ago - 2 comments

#292 - Bump actions/setup-java from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#291 - Rewrite TwoBitWriter using FileChannel and ByteBuffer

Pull Request - State: closed - Opened by athos 11 months ago - 2 comments

#290 - Use ByteBuffer wrapper instead of LSB protocol

Pull Request - State: closed - Opened by athos 11 months ago - 6 comments

#289 - Replacing LSB protocol

Issue - State: closed - Opened by athos 11 months ago - 1 comment

#288 - Disable :missing-docstring linter for test code

Pull Request - State: closed - Opened by athos 11 months ago

#287 - Misc performance tuning for cljam.algo.depth

Pull Request - State: closed - Opened by athos 11 months ago - 1 comment

#286 - Use aset instead of aset-* for performance

Pull Request - State: closed - Opened by athos 12 months ago - 3 comments

#285 - Revert "Bump codecov/codecov-action from 3 to 4"

Pull Request - State: closed - Opened by niyarin 12 months ago

#284 - Bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#283 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#282 - Fix/add doc string

Pull Request - State: closed - Opened by niyarin about 1 year ago - 2 comments
Labels: enhancement

#281 - Fix/shadowing var

Pull Request - State: closed - Opened by niyarin about 1 year ago - 2 comments

#280 - Bump xcoo/clj-lint-action from 1.1.11 to 1.1.12

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#279 - Fix/additional coding style

Pull Request - State: closed - Opened by niyarin over 1 year ago - 2 comments
Labels: enhancement

#278 - Add validator for writing sam.

Pull Request - State: closed - Opened by niyarin over 1 year ago - 1 comment
Labels: enhancement

#277 - Add validator for writing vcf.

Pull Request - State: closed - Opened by niyarin over 1 year ago - 7 comments
Labels: enhancement

#276 - Support explicit first phasing indicator for VCF genotypes

Pull Request - State: closed - Opened by athos over 1 year ago - 1 comment

#275 - Add function for unphasing genotypes

Pull Request - State: closed - Opened by athos over 1 year ago - 1 comment

#274 - Report position in read for reads in a pileup

Issue - State: open - Opened by alumi over 1 year ago
Labels: enhancement

#273 - Coding style fixes from clj-kondo's linter with default :off

Issue - State: closed - Opened by niyarin over 1 year ago

#272 - Fix/vcf float case insensitive

Pull Request - State: closed - Opened by niyarin over 1 year ago - 5 comments

#271 - Features for validating VCF/SAM records

Issue - State: closed - Opened by athos over 1 year ago - 2 comments
Labels: enhancement

#270 - Case insensitive support for NaN/Infinity

Issue - State: closed - Opened by athos over 1 year ago - 2 comments
Labels: bug

#269 - Fix/apply lint

Pull Request - State: closed - Opened by niyarin over 1 year ago - 5 comments

#268 - fix: overflowing qual value in vcf

Pull Request - State: closed - Opened by nuggetoriniku over 1 year ago - 7 comments

#267 - QUAL value overflows when writing VCF

Issue - State: closed - Opened by nuggetoriniku over 1 year ago

#266 - Fix cljam.io.bam-test to work properly

Pull Request - State: closed - Opened by matsutomo81 almost 2 years ago - 3 comments

#265 - Extend the supported data types in encoding alignment options

Pull Request - State: closed - Opened by matsutomo81 about 2 years ago - 1 comment

#264 - Fix error that occurs when encoding a value greater than 32767 with ‘B, S’ data type in encoding alignment in encoding alignment.

Pull Request - State: closed - Opened by matsutomo81 about 2 years ago - 2 comments

#263 - Support CIGARs longer than 65535 operations

Pull Request - State: closed - Opened by matsutomo81 about 2 years ago - 5 comments

#262 - Bump xcoo/clj-lint-action from 1.1.10 to 1.1.11

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#261 - Support CIGARs longer than 65535 operations

Pull Request - State: closed - Opened by matsutomo81 about 2 years ago - 1 comment

#260 - Report position in read for reads in a pileup

Pull Request - State: closed - Opened by DaGaMs over 2 years ago - 2 comments

#259 - bgzipped VCF file over HTTP causes infinite loop

Issue - State: closed - Opened by totakke over 2 years ago - 4 comments
Labels: bug

#258 - Fix to parse VCF meta info key with space

Pull Request - State: closed - Opened by nuggetoriniku over 2 years ago - 4 comments

#257 - Bump actions/setup-java from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#256 - Bump codecov/codecov-action from 2.1.0 to 3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#255 - Bump actions/cache from 2.1.7 to 3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#254 - Bump actions/checkout from 2.4.0 to 3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#253 - Use bgzip as default for writing `.gz` files

Pull Request - State: closed - Opened by alumi almost 3 years ago - 2 comments

#252 - Avoid StackOverflowError while reading a VCF with many lines of meta

Pull Request - State: closed - Opened by k-kom almost 3 years ago - 1 comment
Labels: bug

#251 - Bgziped VCF is illegal.

Issue - State: closed - Opened by niyarin almost 3 years ago - 3 comments

#250 - Bump actions/cache from 2.1.6 to 2.1.7

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#249 - Bump actions/checkout from 2.3.5 to 2.4.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#248 - Bump actions/checkout from 2.3.4 to 2.3.5

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

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

Pull Request - State: closed - Opened by athos about 3 years ago - 3 comments

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

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#245 - Bump codecov/codecov-action from 2.0.3 to 2.1.0

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#244 - Bump codecov/codecov-action from 2.0.2 to 2.0.3

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#243 - Bump codecov/codecov-action from 2.0.1 to 2.0.2

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#242 - Bump codecov/codecov-action from 1.5.2 to 2.0.1

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#241 - Fix parser generation not to interpret unnecessary data when calculat…

Pull Request - State: closed - Opened by niyarin over 3 years ago - 2 comments

#240 - Problem that it takes a long time to create an index file from VCF / BCF with many columns.

Issue - State: closed - Opened by niyarin over 3 years ago

#239 - Fix bam encoder/decoder to convert sam to bam.

Pull Request - State: closed - Opened by niyarin over 3 years ago - 2 comments