ComparativeGenomicsToolkit hal issues

ComparativeGenomicsToolkit / hal

Hierarchical Alignment Format

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Fix hdf5 chunk scaling heuristic for bottom segments

#306 glennhickey opened 2 months ago
0
deprecate hal2mafMP tests, now that tool itself is deprecated

#305 glennhickey closed 2 months ago
0
Fix BottomSegment datatype to store child indexes inside an array

#304 glennhickey closed 2 months ago
0
masking sites in target genome after alignment

#303 JeffWeinell opened 4 months ago
2
halPhyloPMP.py ERROR

#302 bright-hu closed 5 months ago
3
A question about halLiftover

#301 Marh32 opened 5 months ago
5
Error when running halLiftover

#300 zwymic00 opened 5 months ago
2
Be more insistent about cactus-hal2maf

#299 glennhickey closed 6 months ago
0
hal2mafMP.py Cannot allocate memory

#298 bright-hu closed 6 months ago
1
hal make error

#297 Marh32 closed 7 months ago
1
halPhyloP no output or error message?

#296 astarr97 opened 7 months ago
2
Error processing SEQNAME_ARRAY with h5py

#295 bjeight opened 7 months ago
1
Update README to use correct option name for halBranchMutations

#294 yamberk closed 7 months ago
1
new option --bySequence to break down halCoverage by ref sequence

#293 glennhickey closed 6 months ago
0
halRenameGenomes Error

#292 zhangyixing3 closed 8 months ago
1
hal2assemblyhub fails when lifting over `--bedDirs`

#291 brantfaircloth opened 8 months ago
0
hal2maf --length argument does not seem to work properly. Causes incomplete maf output

#290 tli71193 closed 9 months ago
1
Can deletedgenomes or subtree be recovered?

#289 Baohua-Chen opened 9 months ago
2
halUpdateBranchLengths Segmentation fault

#288 francicco closed 10 months ago
2
fix tests

#287 glennhickey closed 11 months ago
0
Error while running HAL make test

#286 Alchimic007 closed 11 months ago
2
hal2maf into vcf

#285 tzaquin opened 11 months ago
3
halLodInterpolate.py --inMemory flag is obsolete but --hdf5InMemory is not recognized

#284 chenhijy closed 11 months ago
4
Small issue with halWriteNucleotides (?fix described)

#283 lukebharrison opened 11 months ago
0
halAlignmentDepth with SNPs

#282 hy09 opened 1 year ago
0
cactus-hal2maf Error

#281 shuifeng1988 opened 1 year ago
2
Add some links and a table of contents to README

#280 glennhickey closed 1 year ago
0
Cleaner Snakes

#279 glennhickey closed 1 year ago
0
Extracting Gene Annotations

#278 tli71193 opened 1 year ago
1
cactus-hal2maf generates incomplete maf result

#277 xiaoyezao opened 1 year ago
6
Intraspecific evolutionary trees

#276 GeorgeBGM closed 1 year ago
1
Fix bug where hdf5 genome internal caches get out of sync and crash

#275 glennhickey closed 1 year ago
0
Help with halPhyloPTrain.py

#274 xiaoyezao opened 1 year ago
7
Speeding up halLiftover

#273 tli71193 closed 1 year ago
5
Detecting synteny among multiple genomes?

#272 aminakur opened 1 year ago
5
Filter species in a hal file

#271 agduncan94 opened 1 year ago
2
specifying a bed interval file for halSnps

#270 tli71193 closed 1 year ago
1
halSnps - extract snps and corresponding coordinates across targetGenomes

#269 nicolo-tellini opened 1 year ago
0
Hal2Maf for PhastCons

#268 francicco opened 1 year ago
0
fix off-by-1 bug when resizing name array

#267 glennhickey closed 1 year ago
1
Fix sequence-name array resizing edge case in renameSequence

#266 twalsh-ebi closed 1 year ago
2
Strand Information in halLiftover

#265 imk1 closed 1 year ago
1
Ortholog Detection?

#264 Jome0169 opened 1 year ago
1
halExtract --root makes corrupt output

#263 glennhickey opened 1 year ago
0
Phast error on MAF file produced by hal2mafMP.py: strand must be + for reference sequence

#262 amizeranschi opened 1 year ago
2
Don't skip already-seen reference positions in hal2maf unless (--unique used).

#261 glennhickey closed 1 year ago
1
patch halAppendSubtree so dimensions always set *before* segments

#260 thiagogenez closed 1 year ago
2
hal2assemblyHub.py fails when using --cladeExclusiveRegions

#259 wodanaz opened 1 year ago
0
add halCloseGenome to C interface

#258 glennhickey closed 1 year ago
0
Avoid reading all genome's sequences when possible

#257 glennhickey closed 1 year ago
0