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Analyzed about 10 hours ago. based on code collected about 10 hours ago.
Aug 17, 2024 — Aug 17, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
add projects.tgbs.bam()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add --join in apps.gsnap.align()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add --snp in apps.gsnap.align()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add projects.tgbs
tanghaibao
as Haibao Tang
More... almost 11 years ago
auto-guess meta in formats.base.write_file()
tanghaibao
as Haibao Tang
More... almost 11 years ago
+ Added ACTION annotation.pasa.assemble() to run PASA alignAssembly + If 2 transcript files are provided (DN & GG), run the PASA compreh trans pipeline + This ACTION be invoked with `--prepare` to generate a run.sh script - The old ACTION annotation.pasa.prepare() is no longer needed + Updated formats.base.write_file() append handling + Updated apps.base.set_align() with some PASA specific alignment params
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
allow gapsize=0 in formats.agp.OO.write_AGP()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add apps.gsnap to wrap GMAP/GSNAP
tanghaibao
as Haibao Tang
More... almost 11 years ago
remove length limitation in fixing AHRD
tanghaibao
as Haibao Tang
More... almost 11 years ago
+ Added ACTION formats.fastq.fromsra() to convert sra to fastq format (this action wraps around the sratoolkit `fastq-dump` command)
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ Renamed SCRIPT apps.entrez to apps.fetch + Renamed ACTION apps.entrez.fetch() to apps.fetch.entrez() + Fixed all imports affected by this rename + Added new ACTION apps.fetch.sra() to download from sra-instant
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ formats.fastq.format() can now convert between different dialects + Users can now specify paired end read tag ("/1" or "/2") to append + Added new fastq dialect: `sra`
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
add more rules to annotaiton.ahrd.fix()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add --fasta in apps.bowtie.align()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add projects.misc.birch()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add compara.synteny.layout()
tanghaibao
as Haibao Tang
More... almost 11 years ago
fix output filename in formats.coords.filter()
tanghaibao
as Haibao Tang
More... almost 11 years ago
fix minor issue with links resetting
tanghaibao
as Haibao Tang
More... almost 11 years ago
add two secret options in assembly.allmaps.path()
tanghaibao
as Haibao Tang
More... almost 11 years ago
modify projects.allmaps.resample() to use logarithmic gradient
tanghaibao
as Haibao Tang
More... almost 11 years ago
add projects.allmaps.resample()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add projects.allmaps.resamplestats()
tanghaibao
as Haibao Tang
More... almost 11 years ago
dynamically set --links when data is sparse
tanghaibao
as Haibao Tang
More... almost 11 years ago
add formats.bed.random()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add --noplot to assembly.allmaps.path()
tanghaibao
as Haibao Tang
More... almost 11 years ago
make assembly.allmaps.path() a pipeline
tanghaibao
as Haibao Tang
More... almost 11 years ago
output set difference in projects.allmaps.comparebed()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add projects.allmaps.comparebed()
tanghaibao
as Haibao Tang
More... almost 11 years ago
handle case when hamiltonian() call fails in assembly.allmaps
tanghaibao
as Haibao Tang
More... almost 11 years ago
rename projects.allmaps.allmapsQC to simulation()
tanghaibao
as Haibao Tang
More... almost 11 years ago