ComparativeGenomicsToolkit/hal issues and pull requests

#314 - Calculate phastCons

Issue - State: closed - Opened by laurafabre about 1 month ago

#313 - fix hdf5 14.4+ runtime errors by relaxing new integrity check

Pull Request - State: closed - Opened by glennhickey about 1 month ago

#312 - Cannot get output from halStats --allCoverage

Issue - State: open - Opened by simone-says about 2 months ago

#311 - Give include.local.mk more control of getting dependencies

Pull Request - State: closed - Opened by diekhans about 2 months ago

#310 - Compile in remote HAL access by default

Issue - State: open - Opened by diekhans 3 months ago

#309 - Build Error with HAL Using HDF5

Issue - State: open - Opened by liangminliu 3 months ago - 5 comments

#308 - GapDeletion

Issue - State: open - Opened by shuiyanwu778 4 months ago - 1 comment

#307 - Unclear conversion extraction subsetting

Issue - State: open - Opened by fgualdr 4 months ago - 1 comment

#306 - Fix hdf5 chunk scaling heuristic for bottom segments

Pull Request - State: closed - Opened by glennhickey 7 months ago

#305 - deprecate hal2mafMP tests, now that tool itself is deprecated

Pull Request - State: closed - Opened by glennhickey 7 months ago

#304 - Fix BottomSegment datatype to store child indexes inside an array

Pull Request - State: closed - Opened by glennhickey 7 months ago

#303 - masking sites in target genome after alignment

Issue - State: open - Opened by JeffWeinell 8 months ago - 2 comments

#302 - halPhyloPMP.py ERROR

Issue - State: closed - Opened by bright-hu 10 months ago - 3 comments

#301 - A question about halLiftover

Issue - State: open - Opened by Marh32 10 months ago - 5 comments

#300 - Error when running halLiftover

Issue - State: open - Opened by zwymic00 10 months ago - 2 comments

#299 - Be more insistent about cactus-hal2maf

Pull Request - State: closed - Opened by glennhickey 11 months ago

#298 - hal2mafMP.py Cannot allocate memory

Issue - State: closed - Opened by bright-hu 11 months ago - 1 comment

#297 - hal make error

Issue - State: closed - Opened by Marh32 12 months ago - 1 comment

#296 - halPhyloP no output or error message?

Issue - State: open - Opened by astarr97 12 months ago - 2 comments

#295 - Error processing SEQNAME_ARRAY with h5py

Issue - State: open - Opened by bjeight 12 months ago - 1 comment

#294 - Update README to use correct option name for halBranchMutations

Pull Request - State: closed - Opened by yamberk about 1 year ago - 1 comment

#293 - new option --bySequence to break down halCoverage by ref sequence

Pull Request - State: closed - Opened by glennhickey about 1 year ago

#292 - halRenameGenomes Error

Issue - State: closed - Opened by zhangyixing3 about 1 year ago - 1 comment

#291 - hal2assemblyhub fails when lifting over `--bedDirs`

Issue - State: open - Opened by brantfaircloth about 1 year ago

#290 - hal2maf --length argument does not seem to work properly. Causes incomplete maf output

Issue - State: closed - Opened by tli71193 about 1 year ago - 1 comment

#289 - Can deletedgenomes or subtree be recovered?

Issue - State: open - Opened by Baohua-Chen about 1 year ago - 2 comments

#288 - halUpdateBranchLengths Segmentation fault

Issue - State: closed - Opened by francicco about 1 year ago - 2 comments

#287 - fix tests

Pull Request - State: closed - Opened by glennhickey over 1 year ago

#286 - Error while running HAL make test

Issue - State: closed - Opened by Alchimic007 over 1 year ago - 2 comments

#285 - hal2maf into vcf

Issue - State: open - Opened by tzaquin over 1 year ago - 3 comments

#284 - halLodInterpolate.py --inMemory flag is obsolete but --hdf5InMemory is not recognized

Issue - State: closed - Opened by chenhijy over 1 year ago - 4 comments

#283 - Small issue with halWriteNucleotides (?fix described)

Issue - State: open - Opened by lukebharrison over 1 year ago

#282 - halAlignmentDepth with SNPs

Issue - State: open - Opened by hy09 over 1 year ago

#281 - cactus-hal2maf Error

Issue - State: open - Opened by shuifeng1988 over 1 year ago - 2 comments

#280 - Add some links and a table of contents to README

Pull Request - State: closed - Opened by glennhickey over 1 year ago

#279 - Cleaner Snakes

Pull Request - State: closed - Opened by glennhickey over 1 year ago

#278 - Extracting Gene Annotations

Issue - State: open - Opened by tli71193 over 1 year ago - 1 comment

#277 - cactus-hal2maf generates incomplete maf result

Issue - State: open - Opened by xiaoyezao over 1 year ago - 6 comments

#276 - Intraspecific evolutionary trees

Issue - State: closed - Opened by George-du over 1 year ago - 1 comment

#275 - Fix bug where hdf5 genome internal caches get out of sync and crash

Pull Request - State: closed - Opened by glennhickey over 1 year ago

#274 - Help with halPhyloPTrain.py

Issue - State: open - Opened by xiaoyezao over 1 year ago - 7 comments

#273 - Speeding up halLiftover

Issue - State: closed - Opened by tli71193 over 1 year ago - 5 comments

#272 - Detecting synteny among multiple genomes?

Issue - State: open - Opened by aminakur over 1 year ago - 5 comments

#271 - Filter species in a hal file

Issue - State: open - Opened by agduncan94 almost 2 years ago - 2 comments

#270 - specifying a bed interval file for halSnps

Issue - State: closed - Opened by tli71193 almost 2 years ago - 1 comment

#269 - halSnps - extract snps and corresponding coordinates across targetGenomes

Issue - State: open - Opened by nicolo-tellini almost 2 years ago - 1 comment

#268 - Hal2Maf for PhastCons

Issue - State: open - Opened by francicco almost 2 years ago

#267 - fix off-by-1 bug when resizing name array

Pull Request - State: closed - Opened by glennhickey almost 2 years ago - 1 comment

#266 - Fix sequence-name array resizing edge case in renameSequence

Pull Request - State: closed - Opened by twalsh-ebi almost 2 years ago - 2 comments

#265 - Strand Information in halLiftover

Issue - State: closed - Opened by imk1 almost 2 years ago - 1 comment

#264 - Ortholog Detection?

Issue - State: open - Opened by Jome0169 almost 2 years ago - 1 comment

#263 - halExtract --root makes corrupt output

Issue - State: open - Opened by glennhickey almost 2 years ago

#262 - Phast error on MAF file produced by hal2mafMP.py: strand must be + for reference sequence

Issue - State: open - Opened by amizeranschi about 2 years ago - 2 comments

#261 - Don't skip already-seen reference positions in hal2maf unless (--unique used).

Pull Request - State: closed - Opened by glennhickey about 2 years ago - 1 comment

#260 - patch halAppendSubtree so dimensions always set before segments

Pull Request - State: closed - Opened by thiagogenez about 2 years ago - 2 comments