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Commits : Listings

Analyzed 1 day ago. based on code collected 1 day ago.
Jul 25, 2024 — Jul 25, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
minor graphics tweaks; allow empty/malformed tracks in graphics.karyotype()
tanghaibao
as Haibao Tang
More... over 12 years ago
add kmer analysis tool to assembly.kmer.histogram(), excerpt from allpaths-lg
tanghaibao
as Haibao Tang
More... over 12 years ago
fix a speed bug in formats.maf.alignment_details() (minor) More... over 12 years ago
add --treefix to apps.phylo.build() More... over 12 years ago
Merge branch 'master' of github.com:tanghaibao/jcvi
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
Allow switching reference and aligned maps in assembly.opticalmap.bed(). Added `append_source` option to append the GFF source name to the bed `accn` field
vivekkrish
as Vivek Krishnakumar
More... over 12 years ago
add legends to annotation.reformat.plot()
tanghaibao
as Haibao Tang
More... over 12 years ago
refactor portions of code from graphics.paper.napusretention() in graphics.chromosome.ChromosomeMap
tanghaibao
as Haibao Tang
More... over 12 years ago
implement prefix spill rules and complete annotation.reformat.instantiate()
tanghaibao
as Haibao Tang
More... over 12 years ago
implement gene name allocator in annotation.reformat.instantiate()
tanghaibao
as Haibao Tang
More... over 12 years ago
refactor name allocation in separate class in annotate.reformat.instantiate()
tanghaibao
as Haibao Tang
More... over 12 years ago
move option --detag into separate function in annotation.reformat.renumber()
tanghaibao
as Haibao Tang
More... over 12 years ago
beautify graphics.paper.napusretention()
tanghaibao
as Haibao Tang
More... over 12 years ago
add assembly.preprocess.count() to count the reads/bases from FASTQC outputs
tanghaibao
as Haibao Tang
More... over 12 years ago
add option --ghost to algorithms.catalog.enrich()
tanghaibao
as Haibao Tang
More... over 12 years ago
add algorithms.catalog.enrich() to enrich results after OMG
tanghaibao
as Haibao Tang
More... over 12 years ago
add --pctid and --pct options in algorithms.catalog.omgprepare() and formats.blast.cscore()
tanghaibao
as Haibao Tang
More... over 12 years ago
enrich figure contents graphics.paper.napusretention()
tanghaibao
as Haibao Tang
More... over 12 years ago
fix bug in apps.last --mask More... over 12 years ago
add graphics.paper.napusretention(); bump up LICENSE year; Happy New Year!
tanghaibao
as Haibao Tang
More... over 12 years ago
fix bugs due to code upgrade in algorithms.synteny
tanghaibao
as Haibao Tang
More... over 12 years ago
place NOTE attributes in mRNA type lines, in formats.genbank.gff()
tanghaibao
as Haibao Tang
More... over 12 years ago
deprecate formats.gff.fromgb()
tanghaibao
as Haibao Tang
More... over 12 years ago
add formats.genbank.gff to convert Genbank file to GFF and FASTA
tanghaibao
as Haibao Tang
More... over 12 years ago
revert to normal behavior when filename list contains only one item in formats.base.must_open()
tanghaibao
as Haibao Tang
More... over 12 years ago
add option --note in formats.gff.format()
tanghaibao
as Haibao Tang
More... over 12 years ago
allow chrUn to be parsed by OMG
tanghaibao
as Haibao Tang
More... over 12 years ago
add annotation.reformat.tRNAscan()
tanghaibao
as Haibao Tang
More... over 12 years ago
bug fix (minor) More... over 12 years ago
typo fix qhighlight->shighlight in graphics.blastplot More... over 12 years ago