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wheretrue
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biobear
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
https://www.wheretrue.dev/docs/exon/biobear/
MIT License
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build(deps): update datafusion requirement from 41 to 43
#183
dependabot[bot]
opened
2 weeks ago
0
build(deps): update noodles requirement from 0.79 to 0.85
#182
dependabot[bot]
opened
2 weeks ago
0
build(deps): update noodles requirement from 0.79 to 0.84
#181
dependabot[bot]
closed
2 weeks ago
1
build(deps): update noodles requirement from 0.79 to 0.83
#180
dependabot[bot]
closed
1 month ago
1
build(deps): update datafusion requirement from 41 to 42
#179
dependabot[bot]
closed
2 weeks ago
1
build(deps): update noodles requirement from 0.79 to 0.82
#178
dependabot[bot]
closed
1 month ago
1
Improve attribute data structure for gtf_scan
#177
jdcla
opened
2 months ago
0
Read all gtf attribute entries when using gtf_scan.
#176
jdcla
closed
2 months ago
1
build(deps): update noodles requirement from 0.79 to 0.81
#175
dependabot[bot]
closed
2 months ago
1
build(deps): update noodles requirement from 0.79 to 0.80
#174
dependabot[bot]
closed
2 months ago
1
build(deps): update exon requirement from 0.31.0 to 0.32.2
#173
dependabot[bot]
opened
2 months ago
0
build(deps): update arrow requirement from 52.1.0 to 53.0.0
#172
dependabot[bot]
opened
2 months ago
0
read bam error
#171
Liripo
closed
2 months ago
6
Error executing FASTQScan
#170
tshauck
opened
2 months ago
0
build: update exon to 0.31
#169
tshauck
closed
3 months ago
0
build(deps): update datafusion requirement from 40 to 41
#168
dependabot[bot]
closed
3 months ago
1
build(deps): update noodles requirement from 0.78 to 0.79
#167
dependabot[bot]
closed
3 months ago
0
feat: finish transition to file options
#166
tshauck
closed
3 months ago
0
feat: remove readers
#165
tshauck
closed
3 months ago
0
Mark Deprecation for Reader Classes
#164
tshauck
closed
3 months ago
0
Can not read ".fq" file
#163
xiasijian
closed
3 months ago
4
fix: logical vs physical plan mismatch
#162
tshauck
closed
3 months ago
0
feat: add sdf read options
#161
tshauck
closed
4 months ago
0
build(deps): update noodles requirement from 0.77 to 0.78
#160
dependabot[bot]
closed
4 months ago
1
build(deps): update exon requirement from 0.26 to 0.28
#159
dependabot[bot]
closed
4 months ago
1
build(deps): update datafusion requirement from 39 to 40
#158
dependabot[bot]
closed
4 months ago
1
build(deps): update pyo3 requirement from 0.21.2 to 0.22.0
#157
dependabot[bot]
opened
5 months ago
0
feat: add bed file option inference
#156
tshauck
closed
5 months ago
0
feat: add gff file extension and compression inference
#155
tshauck
closed
5 months ago
0
Infer extension and compression from file path.
#154
tshauck
opened
5 months ago
0
feat: infer options from file name for fasta and fastq file types
#153
tshauck
closed
5 months ago
0
Why is specifying the extension required when reading files?
#152
ghuls
closed
5 months ago
2
fix: add FastaSequenceDataType import
#151
ghuls
closed
5 months ago
2
Investigate granges rust crate
#150
ghuls
opened
5 months ago
4
build(deps): update noodles requirement from 0.76 to 0.77
#149
dependabot[bot]
closed
5 months ago
0
build: update noodles to support longer BED names (#148)
#148
tshauck
closed
5 months ago
0
Update user docs for new BED options
#147
tshauck
closed
5 months ago
1
feat: support more bed options
#146
tshauck
closed
5 months ago
0
name column in BED file is limited to 255 bytes.
#145
ghuls
closed
5 months ago
6
Support reading BED files with less than 12 column.
#144
ghuls
closed
5 months ago
4
docs: update README for integrations
#143
tshauck
closed
5 months ago
0
build(deps): update datafusion requirement from 38 to 39
#142
dependabot[bot]
closed
5 months ago
1
build(deps): update noodles requirement from 0.74 to 0.76
#141
dependabot[bot]
closed
5 months ago
0
build(deps): update noodles requirement from 0.74 to 0.75
#140
dependabot[bot]
closed
5 months ago
1
feat: update FASTA for encoding and copy
#139
tshauck
closed
5 months ago
0
build(deps): update exon requirement from 0.22.0 to 0.23.0
#138
dependabot[bot]
closed
5 months ago
1
Integer Encoding
#137
tshauck
closed
5 months ago
0
build(deps): update exon requirement from 0.21.1 to 0.22.0
#136
dependabot[bot]
closed
6 months ago
0
fix: new exon to fix overflow
#135
tshauck
closed
6 months ago
0
build(deps): update noodles requirement from 0.73 to 0.74
#134
dependabot[bot]
closed
5 months ago
0
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