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Commits : Listings

Analyzed 1 day ago. based on code collected 1 day ago.
Jul 16, 2024 — Jul 16, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
allow passing highlight regions via command line in graphics.blastplot
Jingping Li
More... over 12 years ago
minor clarification (minor)
Jingping Li
More... over 12 years ago
wrapped lastdb option -c in apps.last
Jingping Li
More... over 12 years ago
added --genefamily in algorithms.catalog.tandem()
Jingping Li
More... over 12 years ago
use need_update to check file existence in apps.bwa
tanghaibao
as Haibao Tang
More... over 12 years ago
add tag OVERLAP in annotation.reformat.renumber()
tanghaibao
as Haibao Tang
More... over 12 years ago
add annotation.reformat.instantiate()
tanghaibao
as Haibao Tang
More... over 12 years ago
add annotation.reformat.renumber()
tanghaibao
as Haibao Tang
More... over 12 years ago
add assembly.gaps.estimate() to estimate gap sizes from mates
tanghaibao
as Haibao Tang
More... over 12 years ago
add algorithms.reconstruct.adjgraph()
tanghaibao
as Haibao Tang
More... over 12 years ago
add --palette to graphics.dotplot and --prefix to algorithms.synteny.summary()
tanghaibao
as Haibao Tang
More... over 12 years ago
allow a different outfile name in formats.blast.filter()
tanghaibao
as Haibao Tang
More... over 12 years ago
minor beautification of apps.uniprot
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
added apps.uniprot to perform batch UniProt queries (makes use of REST API provided by UniProt.org)
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
add formats.sam.consensus() to generate consensus FASTA for a BAM file
tanghaibao
as Haibao Tang
More... over 12 years ago
add --bed in formats.fasta.extract()
Jingping Li
More... over 12 years ago
accommodate long seq names in apps.ks; add --ids in formats.blast to extract records based on seq names
Jingping Li
More... over 12 years ago
add annotation.evm as wrapper for TIGR EVM software
tanghaibao
as Haibao Tang
More... over 12 years ago
add assembly.gaps.sizes() to estimate the gap sizes in an alternative assembly
tanghaibao
as Haibao Tang
More... over 12 years ago
add graphics.xkcd to plot comic plots
tanghaibao
as Haibao Tang
More... over 12 years ago
add new ALLPATHS fastb to fastq function (old is in pairs(), to be deprecated)
tanghaibao
as Haibao Tang
More... over 12 years ago
add --theme to graphics.base.set_image_options(), adding three more fonts with default to Helvetica
tanghaibao
as Haibao Tang
More... over 12 years ago
make append mode explicit in formats.base.must_open(); add --self in formats.blast.filter()
Jingping Li
More... over 12 years ago
fix a bug in formats.blast.BlastSlow.to_dict() (minor)
Jingping Li
More... over 12 years ago
add algorithms.synteny.AnchorFile.blast()
Jingping Li
More... over 12 years ago
add HAPLOIDIFY=True in assembly.allpaths
tanghaibao
as Haibao Tang
More... over 12 years ago
Revert recent change to formats.blast.BlastLine; @Jingping, see my comments to your push
tanghaibao
as Haibao Tang
More... over 12 years ago
allow initialization of BlastLine objects from flexible columns in formats.blast
Jingping Li
More... almost 13 years ago
fix NoneType indexing and color hitchhiking bugs in graphics.tree; refactor some functions in apps.phylo
Jingping Li
More... almost 13 years ago
force pctid check in formats.blast.covfilter()
tanghaibao
as Haibao Tang
More... almost 13 years ago