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ComparativeGenomicsToolkit
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taffy
This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
MIT License
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get_column_iterator SEGV
#66
diekhans
opened
4 days ago
2
making python Alignment objects subscriptable
#65
diekhans
opened
5 days ago
0
move error msg before header
#64
glennhickey
closed
1 month ago
0
error handling when index needed but input stdin
#63
glennhickey
closed
1 month ago
0
taffy view with a --region SEGVs when stdin as input
#62
diekhans
opened
1 month ago
4
bin included
#61
cyborgdnx
opened
3 months ago
0
Update README.md
#60
benedictpaten
closed
3 months ago
0
Refactoring the docs.
#59
benedictpaten
closed
3 months ago
0
fix tai bug where reading past last record could crash
#58
glennhickey
closed
3 months ago
0
dont filter empty rows when doing subrange
#57
glennhickey
closed
3 months ago
0
Option to print BED intervals of reference covered by TAF
#56
glennhickey
closed
3 months ago
0
make sure taf-writing tools all have -sc
#55
glennhickey
closed
3 months ago
0
fix tai to expect (and ignore) tag characters
#54
glennhickey
closed
4 months ago
0
fix invalid region checker to catch 0-length interval
#53
glennhickey
closed
4 months ago
0
Fix index query bug
#52
glennhickey
closed
4 months ago
0
add std=c++11 to cxxflags to hopefully fix mac build
#51
glennhickey
closed
4 months ago
0
Branch for my experiments with DL on alignments
#50
benedictpaten
closed
3 months ago
0
Adds to taffy sort an option to not sort or filter the first row duri…
#49
benedictpaten
closed
3 months ago
1
Fix bug where tai index query could return block with incorrect column_number
#48
glennhickey
closed
5 months ago
0
taffy coverage
#47
glennhickey
closed
5 months ago
0
fix assert error in tai clipping
#46
glennhickey
closed
6 months ago
0
Fix index query bug where overlaps of first position missed
#45
glennhickey
closed
6 months ago
0
add CACTUS_LEGACY_ARCH toggle to disable avx2
#44
glennhickey
closed
6 months ago
0
Update README.md
#43
benedictpaten
closed
6 months ago
0
Update README.md
#42
benedictpaten
closed
6 months ago
0
Use abPOA for gap alignments
#41
glennhickey
closed
6 months ago
5
Fix norm
#40
benedictpaten
closed
6 months ago
1
Support q-lines in MAF
#39
glennhickey
opened
7 months ago
1
taffy norm seems to miss straightforward case
#38
glennhickey
closed
6 months ago
4
Pretty printing
#37
benedictpaten
closed
6 months ago
1
Update README.md
#36
benedictpaten
closed
7 months ago
0
Fix paf export cigar bug
#35
glennhickey
closed
7 months ago
0
Simplify python lib
#34
benedictpaten
closed
7 months ago
0
fix tai test to not need taffy in PATH
#33
glennhickey
closed
7 months ago
0
Fix bug in greedy dupe filter
#32
glennhickey
closed
7 months ago
0
PAF export
#31
glennhickey
closed
10 months ago
0
Fix tai index (again)
#30
glennhickey
closed
1 year ago
0
Fix tai index lookup bug for incomplete chroms
#29
glennhickey
closed
1 year ago
0
fix bug where taffy view -m only worked with -r
#28
glennhickey
closed
1 year ago
0
Add support for on-the-fly genome renaming via input tsv to taffy view
#27
glennhickey
closed
1 year ago
0
Fix up dupe filter in taffy norm
#26
glennhickey
closed
1 year ago
0
Make hts flags overriding a little simpler
#25
glennhickey
closed
1 year ago
0
need an autoconf configure script
#24
diekhans
opened
1 year ago
0
install instruction incorrect
#23
diekhans
opened
1 year ago
0
Allow htslib flags pass-through
#22
glennhickey
closed
1 year ago
0
improve stats tests error messaging
#21
glennhickey
closed
1 year ago
0
fix taffy invocation with rel path
#20
glennhickey
closed
1 year ago
0
Fix merge bug from #18
#19
glennhickey
closed
1 year ago
0
Fix merge conflict from #17
#18
glennhickey
closed
1 year ago
0
Getting python code to build with htslib / adding in column iterators for pyTorch
#17
benedictpaten
closed
1 year ago
0
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