Ecosyste.ms: Issues

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GitHub / ComparativeGenomicsToolkit/taffy issues and pull requests

#66 - get_column_iterator SEGV

Issue - State: open - Opened by diekhans 3 months ago - 2 comments

#65 - making python Alignment objects subscriptable

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

#64 - move error msg before header

Pull Request - State: closed - Opened by glennhickey 4 months ago

#63 - error handling when index needed but input stdin

Pull Request - State: closed - Opened by glennhickey 4 months ago

#62 - taffy view with a --region SEGVs when stdin as input

Issue - State: open - Opened by diekhans 4 months ago - 4 comments

#61 - bin included

Pull Request - State: open - Opened by cyborgdnx 6 months ago

#60 - Update README.md

Pull Request - State: closed - Opened by benedictpaten 6 months ago

#59 - Refactoring the docs.

Pull Request - State: closed - Opened by benedictpaten 6 months ago

#58 - fix tai bug where reading past last record could crash

Pull Request - State: closed - Opened by glennhickey 6 months ago

#57 - dont filter empty rows when doing subrange

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

#56 - Option to print BED intervals of reference covered by TAF

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

#55 - make sure taf-writing tools all have -sc

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

#54 - fix tai to expect (and ignore) tag characters

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

#53 - fix invalid region checker to catch 0-length interval

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

#52 - Fix index query bug

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

#51 - add std=c++11 to cxxflags to hopefully fix mac build

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

#50 - Branch for my experiments with DL on alignments

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

#49 - Adds to taffy sort an option to not sort or filter the first row duri…

Pull Request - State: closed - Opened by benedictpaten 7 months ago - 1 comment

#47 - taffy coverage

Pull Request - State: closed - Opened by glennhickey 8 months ago

#46 - fix assert error in tai clipping

Pull Request - State: closed - Opened by glennhickey 9 months ago

#45 - Fix index query bug where overlaps of first position missed

Pull Request - State: closed - Opened by glennhickey 9 months ago

#44 - add CACTUS_LEGACY_ARCH toggle to disable avx2

Pull Request - State: closed - Opened by glennhickey 9 months ago

#43 - Update README.md

Pull Request - State: closed - Opened by benedictpaten 9 months ago

#42 - Update README.md

Pull Request - State: closed - Opened by benedictpaten 9 months ago

#41 - Use abPOA for gap alignments

Pull Request - State: closed - Opened by glennhickey 9 months ago - 5 comments

#40 - Fix norm

Pull Request - State: closed - Opened by benedictpaten 10 months ago - 1 comment

#39 - Support q-lines in MAF

Pull Request - State: open - Opened by glennhickey 10 months ago - 1 comment

#38 - taffy norm seems to miss straightforward case

Issue - State: closed - Opened by glennhickey 10 months ago - 4 comments

#37 - Pretty printing

Pull Request - State: closed - Opened by benedictpaten 10 months ago - 1 comment

#36 - Update README.md

Pull Request - State: closed - Opened by benedictpaten 10 months ago

#35 - Fix paf export cigar bug

Pull Request - State: closed - Opened by glennhickey 10 months ago

#34 - Simplify python lib

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

#33 - fix tai test to not need taffy in PATH

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

#32 - Fix bug in greedy dupe filter

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

#31 - PAF export

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

#30 - Fix tai index (again)

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

#29 - Fix tai index lookup bug for incomplete chroms

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

#28 - fix bug where taffy view -m only worked with -r

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

#26 - Fix up dupe filter in taffy norm

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

#25 - Make hts flags overriding a little simpler

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

#24 - need an autoconf configure script

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

#23 - install instruction incorrect

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

#22 - Allow htslib flags pass-through

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

#21 - improve stats tests error messaging

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

#20 - fix taffy invocation with rel path

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

#19 - Fix merge bug from #18

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

#18 - Fix merge conflict from #17

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

#16 - Better error msg when opening gzipped input without htslib

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

#15 - WIP : playing with more aggressive normalization

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

#14 - Support MAF indexing

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

#13 - Add taffy stats command

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

#12 - Reduce default index interval size

Pull Request - State: closed - Opened by glennhickey almost 2 years ago - 3 comments

#11 - Add output-format option to taffy view

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

#10 - Tune indexing performance

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

#9 - Clean up anchor line logic

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

#8 - Add blurb on indexing

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

#7 - Adding in method for column iteration

Pull Request - State: closed - Opened by benedictpaten almost 2 years ago

#6 - Adding in support for tai indexes into python lib

Pull Request - State: closed - Opened by benedictpaten almost 2 years ago

#5 - [WIP] Index support

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

#3 - Small fixes to let make test run CGL_DEBUG=ultra

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

#2 - switch to the sonLib in comparativeGenomicsToolkit

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

#1 - Hal support for taf_add_gap_bases

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