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Issues list

Guidance on Extracting Aligned Sequences for Parent and Child Triplets
#316 opened Jan 22, 2025 by YusenHou519
Cannot get output from halStats --allCoverage
#312 opened Dec 22, 2024 by simone-says
Compile in remote HAL access by default
#310 opened Nov 23, 2024 by diekhans
@diekhans
Build Error with HAL Using HDF5
#309 opened Oct 30, 2024 by liangminliu
5
GapDeletion
#308 opened Oct 11, 2024 by shuiyanwu778
1
Unclear conversion extraction subsetting
#307 opened Oct 7, 2024 by fgualdr
1
masking sites in target genome after alignment
#303 opened Jun 4, 2024 by JeffWeinell
2
A question about halLiftover
#301 opened Apr 25, 2024 by Marh32
5
Error when running halLiftover
#300 opened Apr 25, 2024 by zwymic00
2
Error processing SEQNAME_ARRAY with h5py
#295 opened Feb 15, 2024 by bjeight
1
hal2assemblyhub fails when lifting over --bedDirs
#291 opened Jan 17, 2024 by brantfaircloth
Can deletedgenomes or subtree be recovered?
#289 opened Jan 4, 2024 by Baohua-Chen
2
hal2maf into vcf
#285 opened Oct 23, 2023 by tzaquin
3
Small issue with halWriteNucleotides (?fix described)
#283 opened Oct 12, 2023 by lukebharrison
halAlignmentDepth with SNPs
#282 opened Sep 28, 2023 by hy09
cactus-hal2maf Error
#281 opened Sep 24, 2023 by shuifeng1988
2
Extracting Gene Annotations
#278 opened Jul 19, 2023 by tli71193
1
cactus-hal2maf generates incomplete maf result
#277 opened Jun 29, 2023 by xiaoyezao
6
Help with halPhyloPTrain.py
#274 opened Jun 15, 2023 by xiaoyezao
7
Detecting synteny among multiple genomes?
#272 opened May 18, 2023 by aminakur
5
Filter species in a hal file
#271 opened May 4, 2023 by agduncan94
2
halSnps - extract snps and corresponding coordinates across targetGenomes
#269 opened Mar 31, 2023 by nicolo-tellini
1
Hal2Maf for PhastCons
#268 opened Mar 15, 2023 by francicco
Ortholog Detection?
#264 opened Feb 21, 2023 by Jome0169
1
halExtract --root makes corrupt output
#263 opened Feb 17, 2023 by glennhickey
ProTip! no:milestone will show everything without a milestone.