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Commits : Listings

Analyzed 2 days ago. based on code collected 2 days ago.
Aug 21, 2024 — Aug 21, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
add --workdir to assembly.preprocess.correct()
tanghaibao
as Haibao Tang
More... almost 12 years ago
add --tag to formats.fastq.pairinplace()
tanghaibao
as Haibao Tang
More... almost 12 years ago
expose --cutoff in apps.bwa.align()
tanghaibao
as Haibao Tang
More... almost 12 years ago
set default bowtie to run on all data instead of just first 100K reads
tanghaibao
as Haibao Tang
More... almost 12 years ago
change default parameters for TRIMMOMATIC
tanghaibao
as Haibao Tang
More... almost 12 years ago
modify output for formats.fasta.info()
tanghaibao
as Haibao Tang
More... almost 12 years ago
add assembly.preprocess.diginorm() to normalize coverage
tanghaibao
as Haibao Tang
More... almost 12 years ago
simplify formats.fastq.convert()
tanghaibao
as Haibao Tang
More... almost 12 years ago
modify formats.base.FileShredder to test file existence; move fixChromName to utils.cbook
tanghaibao
as Haibao Tang
More... almost 12 years ago
Add option `--fixchrnames` to help fix quirky chromosomes names (from medicago/maize) and normalize them to chr1/2/3, etc. Added formats.gff.fromsoap() to convert soap alignment output to GFF3 format
vivekkrish
as Vivek Krishnakumar
More... almost 12 years ago
add reverse_complement() in assembly.preprocess.expand()
tanghaibao
as Haibao Tang
More... almost 12 years ago
apply recursion in apps.softlink.get_abs_path()
tanghaibao
as Haibao Tang
More... almost 12 years ago
add assembly.preprocess.expand()
tanghaibao
as Haibao Tang
More... almost 12 years ago
use absolute path for building BLAST database
tanghaibao
as Haibao Tang
More... almost 12 years ago
add formats.fasta.info()
tanghaibao
as Haibao Tang
More... almost 12 years ago
add assembly.sspace.close()
tanghaibao
as Haibao Tang
More... almost 12 years ago
add --reorder to apps.bowtie.align(), remove --tidy in apps.vecscreen.mask()
tanghaibao
as Haibao Tang
More... almost 12 years ago
add formats.fastq.catread()
tanghaibao
as Haibao Tang
More... almost 12 years ago
make --local default mode for apps.bowtie.align()
tanghaibao
as Haibao Tang
More... almost 12 years ago
add more options to assembly.automaton.contamination
tanghaibao
as Haibao Tang
More... almost 12 years ago
extract --rclip into apps.base.OptionParser
tanghaibao
as Haibao Tang
More... almost 12 years ago
fix outfile in apps.grid.run
tanghaibao
as Haibao Tang
More... almost 12 years ago
add --pbjelly_home to assembly/pbjelly.py
tanghaibao
as Haibao Tang
More... almost 12 years ago
add assembly.sspace.scaffold() and option --gapclose to assembly.soap.prepare()
tanghaibao
as Haibao Tang
More... almost 12 years ago
Separated DB connection opts to apps.base.OptionParser.set_db_opts(); Updated invocation of actions within utils.sybase. Fixed gffline() within formats.agp.AGPLine; removed the `--nogaps` default when requesting GFF3 output. Updated apps.grid.run() to now allow running a command without having to specify any files to iterate over
vivekkrish
as Vivek Krishnakumar
More... almost 12 years ago
remove --log in apps.bowtie.align()
tanghaibao
as Haibao Tang
More... almost 12 years ago
make absolute path in align() for apps.bowtie and apps.bwa()
tanghaibao
as Haibao Tang
More... almost 12 years ago
allow indexing to happen in the original directory rather than current in apps.bowtie() and apps.bwa()
tanghaibao
as Haibao Tang
More... almost 12 years ago
will not write outfile and errfile if they are empty in apps.grid
tanghaibao
as Haibao Tang
More... almost 12 years ago
check PBS or SBE in apps.grid.get_grid_engine()
tanghaibao
as Haibao Tang
More... almost 12 years ago