| minor graphics tweaks; allow empty/malformed tracks in graphics.karyotype() |
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over 12 years ago
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| add kmer analysis tool to assembly.kmer.histogram(), excerpt from allpaths-lg |
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over 12 years ago
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| fix a speed bug in formats.maf.alignment_details() (minor) |
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over 12 years ago
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| add --treefix to apps.phylo.build() |
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over 12 years ago
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| Merge branch 'master' of github.com:tanghaibao/jcvi |
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over 12 years ago
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| 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 |
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over 12 years ago
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| add legends to annotation.reformat.plot() |
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over 12 years ago
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| refactor portions of code from graphics.paper.napusretention() in graphics.chromosome.ChromosomeMap |
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over 12 years ago
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| implement prefix spill rules and complete annotation.reformat.instantiate() |
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over 12 years ago
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| implement gene name allocator in annotation.reformat.instantiate() |
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over 12 years ago
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| refactor name allocation in separate class in annotate.reformat.instantiate() |
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over 12 years ago
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| move option --detag into separate function in annotation.reformat.renumber() |
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over 12 years ago
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| beautify graphics.paper.napusretention() |
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over 12 years ago
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| add assembly.preprocess.count() to count the reads/bases from FASTQC outputs |
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over 12 years ago
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| add option --ghost to algorithms.catalog.enrich() |
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over 12 years ago
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| add algorithms.catalog.enrich() to enrich results after OMG |
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over 12 years ago
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| add --pctid and --pct options in algorithms.catalog.omgprepare() and formats.blast.cscore() |
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over 12 years ago
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| enrich figure contents graphics.paper.napusretention() |
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over 12 years ago
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| fix bug in apps.last --mask |
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over 12 years ago
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| add graphics.paper.napusretention(); bump up LICENSE year; Happy New Year! |
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over 12 years ago
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| fix bugs due to code upgrade in algorithms.synteny |
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over 12 years ago
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| place NOTE attributes in mRNA type lines, in formats.genbank.gff() |
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over 12 years ago
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| deprecate formats.gff.fromgb() |
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over 12 years ago
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| add formats.genbank.gff to convert Genbank file to GFF and FASTA |
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over 12 years ago
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| revert to normal behavior when filename list contains only one item in formats.base.must_open() |
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over 12 years ago
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| add option --note in formats.gff.format() |
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over 12 years ago
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| allow chrUn to be parsed by OMG |
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over 12 years ago
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| add annotation.reformat.tRNAscan() |
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over 12 years ago
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| bug fix (minor) |
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over 12 years ago
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| typo fix qhighlight->shighlight in graphics.blastplot |
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over 12 years ago
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