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ComparativeGenomicsToolkit
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hal
Hierarchical Alignment Format
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hal2assemblyHub.py fails when using --cladeExclusiveRegions
#259
wodanaz
opened
1 year ago
0
add halCloseGenome to C interface
#258
glennhickey
closed
2 years ago
0
Avoid reading all genome's sequences when possible
#257
glennhickey
closed
2 years ago
0
Adjust default HDF5 caching behaviour
#256
glennhickey
closed
2 years ago
1
add halRemoveSubtree
#255
glennhickey
closed
2 years ago
0
Close neighbors in halExtract to better work with --inMemory
#254
glennhickey
closed
2 years ago
0
More memory fixes for halAppendSubtree
#253
glennhickey
closed
2 years ago
0
Allow halAppendSubtree to be run with --inMemory
#252
glennhickey
closed
2 years ago
0
Add jobstore arg to hal2assemblyHub doc+examples
#251
glennhickey
closed
2 years ago
0
hal2assemblyHub.py parameters Error. For jobStore
#250
LuLiangL
closed
2 years ago
0
remove --tab option from halLiftover
#249
glennhickey
closed
2 years ago
1
use --bedType instead of --outBedVersion
#248
glennhickey
closed
2 years ago
0
Unrecognized option: --outBedVersion
#247
dylansosa
closed
2 years ago
2
BED coordinates invalid in certain input bed lines, but visually, these lines look fine
#246
darencard
closed
2 years ago
4
faToTwoBit: error while loading shared libraries: libkrb5.so.3
#245
dylansosa
closed
2 years ago
3
Trying to set invalid character: -
#244
bredeson
opened
2 years ago
2
fix UDC build
#243
glennhickey
closed
2 years ago
0
corrupted hal files?, gaps in Snake visualization
#242
tdlong
opened
2 years ago
32
Error - Genome::getChild() - child out of range
#241
Zazzyre
closed
2 years ago
1
fixing topSegments of insertName's node (again)
#240
thiagogenez
closed
2 years ago
2
patch halAddToBranch so dimensions always set *before* segments
#239
glennhickey
closed
2 years ago
0
fix typo that was hidden by NDEBUG
#238
glennhickey
closed
2 years ago
0
Fix PAF so snps and gaps included in cols 10 and 11, resp.
#237
glennhickey
closed
2 years ago
0
patch halReplaceGenomes so dimensions always set *before* segments
#236
glennhickey
closed
2 years ago
0
Error building hal
#235
Zazzyre
opened
2 years ago
3
Release 2.2
#234
glennhickey
closed
2 years ago
0
please tag new release version
#233
EricDeveaud
closed
2 years ago
1
rules.mk does not define RANLIB
#232
EricDeveaud
opened
2 years ago
1
halPhyloP error
#231
francicco
opened
2 years ago
0
phastCons scripts
#230
francicco
opened
3 years ago
0
Input checker for halAddToBranch etc
#229
glennhickey
opened
3 years ago
0
write MAF header when outputting to a stream
#228
diekhans
closed
3 years ago
0
hal2maf doesn't add #maf header when output is to magic name stdout
#227
diekhans
closed
3 years ago
1
changed logic of psl construction in case strands are different
#226
ksenia-krasheninnikova
closed
3 years ago
0
halSynteny sometimes produces invalid PSLs
#225
mhaukness-ucsc
closed
3 years ago
0
hal2maf - option to exclude _MINIGRAPH_ sequences
#224
0xaf1f
opened
3 years ago
0
halPhyloPTrain can't run phyloFit
#223
RenzoTale88
opened
3 years ago
1
halBranchMutations question
#222
zhangyuxin1012
opened
3 years ago
0
Extract single-base alignment for a pair of genomes
#221
RenzoTale88
closed
3 years ago
4
Coverage differs by --length and --start in maf result of hal2maf
#220
pskvins
closed
3 years ago
2
halLiftover vs UCSC liftover
#219
mglgnn
opened
3 years ago
1
hal2mafMP.py speed issue
#218
pskvins
opened
3 years ago
0
PHAST & UDC build
#217
diekhans
closed
3 years ago
0
hal2mafMP.py SyntaxError: leading zeros in decimal integer literals
#216
amv33576
closed
2 years ago
3
Fix hal2assemblyHub
#215
glennhickey
closed
3 years ago
0
Specify phast commit in README
#214
glennhickey
closed
3 years ago
0
How to get output URL for hal2assemblyHub.py?
#213
Solenyalyl
opened
3 years ago
3
Support large numbers of children
#212
glennhickey
closed
4 months ago
14
HAL doesn't compile
#211
jrvalverde
opened
3 years ago
0
HAL Replacegenome failed halValidate
#210
EdYSChuang815
opened
3 years ago
0
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