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Commits : Listings

Analyzed about 6 hours ago. based on code collected about 6 hours ago.
Jul 28, 2024 — Jul 28, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
add algorithms.fractionation.gffselect()
tanghaibao
as Haibao Tang
More... over 12 years ago
add options --synonymous and --fourfold to apps.phylo.build() to subset sequence alignment More... over 12 years ago
add algorithms.fractionation.validate() to confirm the gene loss has no CDS overlaps
tanghaibao
as Haibao Tang
More... over 12 years ago
Augment annotation.reformat.annotate() to now allow assignment of identifiers based on `overlap` length in addition to the global sequence `alignment` score
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
add option --upper to formats.fasta.format()
tanghaibao
as Haibao Tang
More... over 12 years ago
allow --scaffold option in assembly.soap.prepare(); move cscore filtering before tandem removal in apps.blastfilter(); allow algorithms.synteny.liftover() to lift anchor pairs outside the initial bounding box.
tanghaibao
as Haibao Tang
More... over 12 years ago
add option --newfasta to assembly.postprocess.screen()
tanghaibao
as Haibao Tang
More... over 12 years ago
rename assembly.finish to assembly.postprocess and add function screen()
tanghaibao
as Haibao Tang
More... over 12 years ago
Merge branch 'master' of github.com:tanghaibao/jcvi
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
Added functionality to formats.gff.format() to allow modification of GFF source field based on a two-column mapping file. Updated annotation.ahrd.fix() to retain and transfer any IPR and GO terms from the original AHRD to the fixed AHRD csv file
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
add option --tag in formats.gff.extract()
tanghaibao
as Haibao Tang
More... over 12 years ago
Minor update to formats.gff.format() which avoids introducting an empty `Name` attribute into the 9th column of the GFF file when trying to add a note field. Make `pvalue` field of BtabLine in formats.btab optional
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
adjust filesplitter zero-padding
tanghaibao
as Haibao Tang
More... over 12 years ago
make gaps.bed optional in annotation.reformat.rename()
tanghaibao
as Haibao Tang
More... over 12 years ago
Fix logic in the conditional statement that checks to see if an identifier from the `old.bed` file is being assigned to a gene model in the `new.bed` file which resides on a different reference sequence
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
Added annotation.reformat.annotate() to annotate new gene model set with identifiers from an old set; using pybedtools; pipeline relies on Needleman-Wunsch alignment scores to resolve ambiguous loci; will update pipeline to directly call apps.emboss.needle() once multiprocessing is implemented. Fixed module imports in assembly.deconvolute. Added new options to formats.bed.mergeBed()
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
minor modifications in the header fonts in graphics.histogram()
tanghaibao
as Haibao Tang
More... over 12 years ago
add algorithms.fractionation.gaps()
tanghaibao
as Haibao Tang
More... over 12 years ago
add algorithms.fractionation.status() and summary()
tanghaibao
as Haibao Tang
More... over 12 years ago
change algorithms.catalog.ortholog() pipeline - now perform quota first then liftover
tanghaibao
as Haibao Tang
More... over 12 years ago
handles no signal case in read_block()
tanghaibao
as Haibao Tang
More... over 12 years ago
typo in assembly.kmer.histogram()
tanghaibao
as Haibao Tang
More... over 12 years ago
simplify assembly.kmer.histogram()
tanghaibao
as Haibao Tang
More... over 12 years ago
make apps.bwa only output the best alignment (-n 1)
tanghaibao
as Haibao Tang
More... over 12 years ago
simplify formats.fastq.first()
tanghaibao
as Haibao Tang
More... over 12 years ago
add --evalue to apps.base.blast()
tanghaibao
as Haibao Tang
More... over 12 years ago
add apps.emboss to run EMBOSS applications
tanghaibao
as Haibao Tang
More... over 12 years ago
make apps.base py2.5 compatible
tanghaibao
as Haibao Tang
More... over 12 years ago
Update formats.gff.format() --unique option to track any duplicate `ID` which is a `Parent` of another feature and appropriately change the `Parent` field of that feature to reflect the new unique `ID`. Add new RegExp to fix TAIR10 headers
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
flip reads when output mate pair fastq in assembly.preprocess.correct()
tanghaibao
as Haibao Tang
More... over 12 years ago