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Commits : Listings

Analyzed about 17 hours ago. based on code collected about 17 hours ago.
Aug 19, 2024 — Aug 19, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
add graphics.align.PairwiseAlign
tanghaibao
as Haibao Tang
More... almost 11 years ago
add graphics.align
tanghaibao
as Haibao Tang
More... almost 11 years ago
- Remove splicing action from annotation.pasa() (NOT IMPLEMENTED YET)
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ Added annotation.pasa.compare() to run PASA annot compare pipeline + Consolidate pasa_opts into apps.base.OptionParser.set_pasa_opts()
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
add assembly.opticalmap.silicosoma()
tanghaibao
as Haibao Tang
More... almost 11 years ago
change trinity default min_contig_size to 90
tanghaibao
as Haibao Tang
More... almost 11 years ago
+ Fix PASA compreh transcriptome step
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ Fix typo in annotation.pasa.assemble()
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ Minor fixes to annotation.pasa.assemble() + Added PATH to tgi tools in apps.base.set_home()
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
add --depth to projects.tgbs.novo()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add diginorm to projects.tgbs.novo()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add apps.cdhit.uclust() and projects.tgbs.merge()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add --idonly in formats.fasta.extract()
tanghaibao
as Haibao Tang
More... almost 11 years ago
+ Fix trinity.prepare() --grid_conf_file parameter usage (set default)
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ Minor fix to email sending by the `waitpid` notifier
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ Allowing adding `/1 or /2` tag w/o fastq format conversion + Account for slight variations in `sra` fastq format
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ Added apps.trinity.prepare() action which consolidates DN and GG - Remove apps.trinity.dn and gg ACTIONs + Reorganize trinity options in apps.base.set_trinty_opts()
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ Fix trinity-gg command builder to account for multiple input fastq files
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
add projects.tgbs.novo()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add maxlen=1 in apps.cdhit.deduplicate()
tanghaibao
as Haibao Tang
More... almost 11 years ago
add --consensus to apps.cdhit.deduplicate()
tanghaibao
as Haibao Tang
More... almost 11 years ago
+ Added oracle support to utils.db.query() action
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ In apps.trinty.gg(), reads are required along with coord-sorted bam
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ Extended functionality of `--sequential` param in formats.fasta.format() + Modified assembly.trinity.dn() file globbing to match patters used for trinity.gg()
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
+ Add assembly.trinity.gg() action to wrap around the Trinity-GG pipeline + Generalize trinity_opts and add to apps.base() for reusability + Fix off-by-one error in bed->gff conversion
vivekkrish
as Vivek Krishnakumar
More... almost 11 years ago
add bracket to except in graphics.base
tanghaibao
as Haibao Tang
More... almost 11 years ago
version 0.4.10
tanghaibao
as Haibao Tang
More... almost 11 years ago
add formats.base.pairwise()
tanghaibao
as Haibao Tang
More... almost 11 years ago
fix dbfile in apps.bowtie and apps.bwa
tanghaibao
as Haibao Tang
More... almost 11 years ago
add --single to assembly.preprocess.diginorm()
tanghaibao
as Haibao Tang
More... almost 11 years ago