CHANGELOG.md

CHANGELOG

v0.32.2 (2024-09-04)

Fix

• include read_deltalake feature (#623)

v0.32.1 (2024-09-03)

Fix

• remove lightmotif (#622)

v0.32.0 (2024-09-03)

Feat

• support delta tables (#621)

Fix

• better error message for bam reader (#615)
• fix a few bugs (#614)

v0.31.0 (2024-08-17)

Feat

• update noodles (#596)

Fix

• new lock file

v0.30.1 (2024-07-31)

Fix

• update time for cli

v0.30.0 (2024-07-31)

Feat

• use cli context (#586)
• use projection in fastq reads (#584)

Fix

• set mzml compression (#591)
• fix toml
• fix benchmarks

v0.29.1 (2024-07-16)

Fix

• add public with_file_extension
• better header handling
• remove eprintln

v0.29.0 (2024-07-15)

Feat

• add read_sdf api (#576)

v0.28.1 (2024-07-15)

v0.28.0 (2024-07-15)

v0.27.1 (2024-07-15)

v0.27.0 (2024-07-15)

Feat

• update to df 40 (#575)
• support async sdf files (#572)
• update bigwig (#569)
• start adding sdf (#567)
• sdf: array and batch reader (#562)
• add sd reader (#556)
• include data in sd file parsing (#555)

v0.26.1 (2024-06-24)

Feat

• molfile record parser (#553)
• make hmm dom tab extension settable (#547)

Refactor

• fasta options refactor (#544)

v0.26.0 (2024-06-18)

Feat

• support bed files with commented lines (#539)

v0.25.1 (2024-06-17)

v0.25.0 (2024-06-14)

Feat

• support number of fields in bed files (#533)

v0.24.1 (2024-05-30)

Fix

• support relative paths (#522)

v0.24.0 (2024-05-30)

Feat

• support gzip writer (#519)

Refactor

• improve FASTA batch serialization add FASTQ (#520)
• use i8 for sequence integer encoding

v0.23.0 (2024-05-27)

Feat

• copy to FASTA file (#514)

Fix

• sync -> sink (#517)

v0.22.2 (2024-05-25)

Fix

• remove config extraction

Refactor

• re-export data type

v0.22.1 (2024-05-24)

Fix

• better handling for ambiguous AAs

v0.22.0 (2024-05-23)

Feat

• pass through encoding option to create table (#512)
• add integer dna and protein encoding (#511)

Refactor

• one hot to int encode (#513)

v0.21.1 (2024-05-20)

Fix

• fix overflow in position conversion error

v0.21.0 (2024-05-16)

Feat

• add lazy gff support (#505)
• R: expose to_record_batch_reader (#498)
• add dead code (#496)

v0.20.0 (2024-04-24)

Feat

• update vcf table options (#488)

v0.19.1 (2024-04-23)

Fix

• expose crate

v0.19.0 (2024-04-23)

Feat

• add read_cram and read_fcs methods (#487)

v0.18.0 (2024-04-22)

Feat

• simplify genbank schema (#485)

v0.17.0 (2024-04-22)

Feat

• simplify mzml reader

v0.16.7 (2024-04-22)

Refactor

• use ExonArrayBuilder for bcf (#484)

v0.16.6 (2024-04-18)

Fix

• various fixes for biobear side (#481)

v0.16.5 (2024-04-18)

Fix

• update noodles

v0.16.4 (2024-04-17)

Fix

• re-export ExonError

v0.16.3 (2024-04-17)

Fix

• fix release script

v0.16.2 (2024-04-17)

Refactor

• improve config for motif-udfs

v0.16.1 (2024-04-16)

Fix

• fix featurization

v0.16.0 (2024-04-16)

Feat

• bigwig partition and method (#473)
• add bigwig value (#472)
• region filtering for bigwig zoom (#471)
• zoom table scan (#470)
• initial bigwig batch reader (#469)
• add integer_encoding (#466)
• support gff3 extensions (#454)

Refactor

• move bigwig zoom value to new setup (#477)
• simplify options (#476)

v0.15.0 (2024-03-27)

Feat

• add regex positional match (#453)
• support options for file extension in fasta and fastq (#448)
• cram: use reference if available
• cram: return reference name vs stringified id (#446)
• cram: support all fields (#443)
• basic cram execution (#442)

v0.14.0 (2024-03-14)

Feat

• update exon to v13 (#437)

Fix

• remove rust bio dep (#439)

v0.13.0 (2024-03-10)

Feat

• exonr: updating exonr version (#435)

v0.12.0 (2024-03-10)

Feat

• ic for alignment score (#433)
• support local gzipped index (#432)
• better reverse_complement (#431)
• add polya trimming (#428)
• add two new UDFs (#427)

Fix

• remove unwraps

v0.11.1 (2024-03-03)

Feat

• support s3 region files (#420)
• update (#418)
• working with region file (#415)

Fix

• fix tests (#421)

Refactor

• cleanup for point release (#422)

v0.11.0 (2024-02-28)

Feat

• add more code to python (#414)
• move python code into proper (#413)
• add better read_fastq and read_fasta methods (#412)

v0.10.0 (2024-02-25)

Feat

• Add basic indexed FASTA (#409)

v0.9.3 (2024-02-08)

v0.9.2 (2024-02-08)

Feat

• handle extra semiquote in gff (#399)

Refactor

• exonr: use error (#396)

v0.9.1 (2024-02-07)

v0.9.0 (2024-02-07)

Feat

• more datatypes (#390)
• update fastx readers for speed (#388)
• remove justfile (#382)
• basic support for inferred BAM tag fields (#381)
• support large strings (#377)

Fix

• fix ignore on test (#378)

Refactor

• use dedicated struct of bgzf offsets (#385)
• move save out of exon-core (#379)

v0.8.6 (2024-01-29)

Refactor

• remove vcf unwraps (#373)

v0.8.5 (2024-01-28)

Fix

• fix issue parsing broad file (#372)
• update tests (#371)

Refactor

• remove some unwraps (#370)

v0.8.4 (2024-01-27)

Fix

• support bgzip for fastq (#368)
• fix settings extractions (#367)

v0.8.3 (2024-01-26)

Fix

• update BAM/SAM tests (#366)

v0.8.2 (2024-01-25)

v0.8.1 (2024-01-25)

v0.8.0 (2024-01-23)

Feat

• register copy to target
• vcf improvements

Refactor

• update for df 35

v0.7.1 (2024-01-11)

v0.7.0 (2024-01-10)

Feat

• improve s3 handling (#349)
• better nextflow setup (#348)

Fix

• add missing feature

v0.6.0 (2024-01-02)

Feat

• add indexed gff table (#335)
• indexed gff file

Fix

• fix path

v0.5.5 (2023-12-17)

Feat

• support additional file types
• add indexed vcf
• add indexed bam
• add bcf scan function
• add vcf
• add sam scan fun
• bam udf
• add mzml scan function
• add fcs scan
• add genbank scan
• add hmm_dom_tab_scan
• add bed
• add gtf scan
• add gff scan fun
• add fastq scan fun
• add optional arg for compression

Fix

• fix count bug
• fix up error message
• fix aws dep for exon-io

Refactor

• no unwrap in bin vectors
• more general names
• remove bcf/vcf
• separate genbank
• refactor fcs
• pull out mzml parser
• remove DEFAULT_BATCH_SIZE
• generalize scan function
• update to new datafusion

v0.5.4 (2023-12-13)

Refactor

• fixup from removal
• remove exome (#326)

v0.5.3 (2023-11-28)

v0.5.2 (2023-11-28)

v0.5.1 (2023-11-28)

v0.5.0 (2023-11-28)

Feat

• core: use datafusion repartitioning (#314)

Fix

• empty projections (#313)

v0.4.3 (2023-11-27)

Fix

• get extension properly (#311)

v0.4.2 (2023-11-27)

v0.4.1 (2023-11-27)

v0.4.0 (2023-11-27)

Feat

• add core to bed

Fix

• exome: add back tls option (#309)

v0.3.12 (2023-11-26)

Feat

• exome: tweak connection
• exome: add exome options (#306)

Refactor

• move out bed (#304)
• move out gtf file reading (#303)

v0.3.11 (2023-11-20)

Fix

• fix bcf stats bug (#296)

v0.3.10 (2023-11-19)

Feat

• update df to 33 (#288)
• bump noodles
• update r version
• better exonr error handling (#282)
• add test for r to data.frame (#277)
• update exon in R package (#274)
• add exome error type (#270)
• create TableSchema (#268)
• release notes

Fix

• dont clobber phys optimizers (#289)
• fix test syntax

Refactor

• separate out fastq batch reader (#283)
• exome error (#275)
• add code (#271)

v0.3.9 (2023-11-07)

Feat

• refactor partition optimization (#263)

v0.3.8 (2023-11-07)

Fix

• remove union (#262)

v0.3.8-beta.4 (2023-11-06)

v0.3.8-beta.2 (2023-11-06)

Feat

• add sam scan (#261)
• pushdown for bam (#260)
• update bcf pruning (#259)
• fcs projection pruning (#258)
• add hmm partition pruning (#257)
• update aws bits (#256)
• add mzml (#251)
• add bed partition pruning (#249)
• vcf partition pushdown (#246)
• refactor to file partition (#245)
• add fastq pruning tests (#244)
• refactor hive pushdown + fasta (#243)

v0.3.6 (2023-10-30)

v0.3.5 (2023-10-30)

Feat

• prune gff partitions with pushdown (#241)

v0.3.4-beta.12 (2023-10-30)

v0.3.4-beta.11 (2023-10-30)

Feat

• better error messages (#239)
• add partition cols to table schema (#237)

v0.3.4 (2023-10-29)

Feat

• cleanup docs

v0.3.4-beta.10 (2023-10-29)

Feat

• create statement works (#238)
• add descriptions
• updates for exome support (#234)
• start of gff hive parititoning (#231)
• update exonR for duckdb compat (#226)
• add exone-exome (#225)
• refactoring file listing (#222)
• add projection to unindexed case
• support bam repartitioning
• add vcf position tracking
• track read sequences (#205)
• update exonpy
• small tweaks
• better error messages (#203)
• add vcf region filter (#201)
• add bam pushdown (#195)
• pass down bam filter (#192)
• add tags to bam (#188)
• add start/end interval for bam/sam/cram (#186)
• update exome (#184)
• add sqllogictests for fasta/fastq (#181)
• add indexed file type (#179)
• flight con works (#177)
• separate indexed reader (#176)
• support region filters in larger tree (#175)
• connection (#164)
• setup proto for server con (#163)
• add connect method (#160)
• support table compression in exome client (#157)
• streaming bgzf vcf scans (#151)
• get next chunk (#149)
• add back query vcf method on ctx (#148)
• configurable allocation size (#142)
• add capacity (#138)
• chrom eq works (#135)
• make interval optional w/ region expr (#134)
• improve feature rewriting (#133)
• update benchmarks (#130)
• add settings plus testing (#128)
• fixup push downs (#125)
• lazy vcf parsing (#122)
• better FASTA perf, better docs (#121)
• add between rewrite (#113)
• repartition with rule (#108)
• add mzml to R (#89)
• add config with smarter defaults (#86)
• add file-parallelism to other files (#85)
• add fasta parallelism (#83)
• update df to 28
• fixes from mzml pocs (#81)
• contains peak filter (#80)
• adding initial setup for exome service (#75)
• allow some missing mzml files (#63)
• add udfs (#62)
• add mass spec binning (#60)
• fix byteorder import
• cleanup schema (#54)
• add error handling (#53)
• working fcs datasource (#50)
• add fcs reader (#47)
• early warn on bad creds
• handle path in registration
• add aws default chain (#44)
• updating versions (#42)

Fix

• fix clippy
• include protocol for flight conn (#165)
• bgzf uncomperssed offset (#140)
• fix the benchmark (#136)
• add back info/format fields (#123)
• export mzml file
• fix genbank feature flag
• fix AWS_PROFILE (#51)
• cleanup smoke test
• fix feature tag for gcp
• correct schema

Refactor

• pull out FASTA (#220)
• create core package
• refactor session setup
• remove BAM array builder (#191)
• update chrom expr to handle generic fields (#185)
• refactor vcf reader (#171)
• more cleanup (#150)
• add register vcf (#137)

v0.2.3 (2023-07-05)

v0.2.2 (2023-07-05)

v0.2.1 (2023-07-05)

Feat

• refactor r functions (#28)
• filling out r funcs (#27)
• add spectra cv params (#26)
• ic for R lib (#25)
• add precusor/isolation window (#24)
• adding array to mzml (#22)
• add scan and precursor lists to spectrum (#21)
• add bcf querying (#18)
• add register function on context (#17)
• add register function on context (#16)
• add gtf source (#14)
• cleanup benchmars (#13)
• add bam query (#11)
• local vcf query (#10)
• add first samflag (#8)
• gc content (#6)
• ic of udf (#5)
• add Display trait for TCAFileType
• ic

Fix

• fix null, add benchs (#39)
• fix bug when no precursors (#30)
• add missing gtf to sources list (#23)
• dont fail on bad directive (#15)

Refactor

• rename to exon