 STEIMLE Thomas
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ff6cea3cb3
Use local Cargo config for Windows htslib patches
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2 viikkoa sitten |
 Thomas
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334057b7e1
merge
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2 viikkoa sitten |
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STEIMLE Thomas
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1fcf1c5c22
Apply formatting cleanup
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2 viikkoa sitten |
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STEIMLE Thomas
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52d9e6486b
Add block-compressed Pandora variant index
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2 viikkoa sitten |
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STEIMLE Thomas
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fdc969a486
Add Pandora reader and Windows curl patch
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2 viikkoa sitten |
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STEIMLE Thomas
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87009c3474
Add Pandora SomaticPipe output container
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2 viikkoa sitten |
|
Thomas
|
4bbbc66981
Introducing new executor that takes a Vec<Vec<AnyJob>> and treat the inner vec as a sequence.jobs_seq![..] helps to define this sequence from any job that implement LocalRunner and SbatchRunner. ClairS implementation and new resume chunked (TODO: add clairs_allow_resume in config.
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1 kuukausi sitten |
|
Thomas
|
1c81c5bf58
update longcallD merge BAM
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1 kuukausi sitten |
|
Thomas
|
bf12d05d90
longcallD
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1 kuukausi sitten |
|
Thomas
|
3ea0a26d87
multiallelic normalization (just for INFO FREQ of dbsnp) for fetch_vcf, prefer normalized vcf...
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1 kuukausi sitten |
|
Thomas
|
a0f6db44b0
multiallelic normalization (just for INFO FREQ of dbsnp) for fetch_vcf, prefer normalized vcf...
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1 kuukausi sitten |
|
Thomas
|
a1ab3e9dc6
dbg
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1 kuukausi sitten |
|
Thomas
|
f685632548
dbg
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1 kuukausi sitten |
|
Thomas
|
3e63458572
merge
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1 kuukausi sitten |
|
Thomas
|
7abe30225b
ok
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1 kuukausi sitten |
|
Thomas
|
e8875b045d
audit io helpers
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1 kuukausi sitten |
|
Thomas
|
bd5f0f912a
fix vcf_variant.rs: liftover position overflow and redundant allocation
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1 kuukausi sitten |
|
Thomas
|
80432a5436
fix three bugs in variant module
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1 kuukausi sitten |
|
Thomas
|
9fe2d09789
fix variant duplication bug in Variants::merge
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1 kuukausi sitten |
|
Thomas
|
e4ef7537d2
add //! module header to io/mod.rs; fix fastq.rs buffering
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1 kuukausi sitten |
|
Thomas
|
2d9b97dcea
fix and audit fasta.rs, gff.rs, liftover.rs
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1 kuukausi sitten |
|
Thomas
|
f3d94897a1
audit and refactor src/io/pod5_infos.rs
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1 kuukausi sitten |
|
Thomas
|
11ec9f65cd
fix and audit src/io/straglr.rs
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1 kuukausi sitten |
|
Thomas
|
e55bc1d745
ditch csv crate from all non-serde paths
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1 kuukausi sitten |
|
Thomas
|
8198808748
replace csv::ByteRecord + tsv_reader with TsvLine in scan and variants
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1 kuukausi sitten |
|
Thomas
|
f1212b39b4
refactor modkit.rs: drop full-file load, use tabix per-region fetch
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1 kuukausi sitten |
|
Thomas
|
7ce17964e9
audit and refactor src/io/modkit.rs
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1 kuukausi sitten |
|
Thomas
|
1b42565a2f
fix vcf.rs module doc: add fetch_vcf to header table
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1 kuukausi sitten |
|
Thomas
|
8806fc5b0a
add tabix region fetch: fetch_tabix_lines_with, fetch_bed, fetch_vcf
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1 kuukausi sitten |
|
Thomas
|
bceb3174ad
audit and refactor src/io/vcf.rs
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1 kuukausi sitten |
