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Issues list

hal2assemblyhub.py: A Toil workflow can only be started once. Use Toil.restart() to resume it.
#317 opened Feb 3, 2025 by twooldridge updated Feb 26, 2025
1
Rename .hal file species
#318 opened Feb 6, 2025 by msGreen98 updated Feb 26, 2025
2
Guidance on Extracting Aligned Sequences for Parent and Child Triplets
#316 opened Jan 22, 2025 by YusenHou519 updated Jan 22, 2025
Compile in remote HAL access by default
#310 opened Nov 23, 2024 by diekhans updated Nov 23, 2024
@diekhans
halSnps - extract snps and corresponding coordinates across targetGenomes
#269 opened Mar 31, 2023 by nicolo-tellini updated Nov 11, 2024
1
Build Error with HAL Using HDF5
#309 opened Oct 30, 2024 by liangminliu updated Nov 1, 2024
5
GapDeletion
#308 opened Oct 11, 2024 by shuiyanwu778 updated Oct 11, 2024
1
Unclear conversion extraction subsetting
#307 opened Oct 7, 2024 by fgualdr updated Oct 7, 2024
1
masking sites in target genome after alignment
#303 opened Jun 4, 2024 by JeffWeinell updated Jun 4, 2024
2
Detecting synteny among multiple genomes?
#272 opened May 18, 2023 by aminakur updated May 31, 2024
5
A question about halLiftover
#301 opened Apr 25, 2024 by Marh32 updated Apr 30, 2024
5
Error when running halLiftover
#300 opened Apr 25, 2024 by zwymic00 updated Apr 26, 2024
2
Error processing SEQNAME_ARRAY with h5py
#295 opened Feb 15, 2024 by bjeight updated Feb 15, 2024
1
hal2assemblyhub fails when lifting over --bedDirs
#291 opened Jan 17, 2024 by brantfaircloth updated Jan 17, 2024
Can deletedgenomes or subtree be recovered?
#289 opened Jan 4, 2024 by Baohua-Chen updated Jan 6, 2024
2
hal2maf into vcf
#285 opened Oct 23, 2023 by tzaquin updated Oct 24, 2023
3
Small issue with halWriteNucleotides (?fix described)
#283 opened Oct 12, 2023 by lukebharrison updated Oct 12, 2023
halAlignmentDepth with SNPs
#282 opened Sep 28, 2023 by hy09 updated Sep 28, 2023
cactus-hal2maf Error
#281 opened Sep 24, 2023 by shuifeng1988 updated Sep 25, 2023
2
Extracting Gene Annotations
#278 opened Jul 19, 2023 by tli71193 updated Jul 24, 2023
1
Help with halPhyloPTrain.py
#274 opened Jun 15, 2023 by xiaoyezao updated Jul 4, 2023
7
cactus-hal2maf generates incomplete maf result
#277 opened Jun 29, 2023 by xiaoyezao updated Jun 30, 2023
6
hal2chain for faster halLiftover
#193 opened Feb 15, 2021 by badoi updated May 16, 2023
@diekhans
5
Filter species in a hal file
#271 opened May 4, 2023 by agduncan94 updated May 5, 2023
2
Ortholog Detection?
#264 opened Feb 21, 2023 by Jome0169 updated Mar 17, 2023
1
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