| use --cmap in graphics.dotplot |
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over 10 years ago
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| add option --contigs in assembly.ca.graph() |
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over 10 years ago
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| add formats.bed.density() |
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over 10 years ago
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| add graphics.assembly.covlen() |
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over 10 years ago
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| change --self to --noself in formats.blast.filter() |
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over 10 years ago
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| add assembly.ca.overlap(), remove assembly.ca.bisect() |
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over 10 years ago
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| modify --isoform in formats.gff.summary() |
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over 10 years ago
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| pickle graph to disk in assembly.ca.graph() |
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over 10 years ago
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| rename apps.gsnap to apps.gmap |
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over 10 years ago
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| add formats.bed.clr() |
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over 10 years ago
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| + Add ability to perform non-strict parsing of GFF |
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over 10 years ago
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| add assembly.kmer.model() |
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over 10 years ago
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| add scrutinizer badges |
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over 10 years ago
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| add --sorted in projects.tgbs.track() |
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over 10 years ago
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| + Add option to formats.gff.format() to remove features by ID + Add new method gff.fixboundaries() to help adjust boundaries of certain feature types based on the child features |
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over 10 years ago
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| write both clean table and te table in projects.pineapple.geneinfo() |
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over 10 years ago
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| add --extra to graphics.synteny and projects.misc.oropetium() |
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over 10 years ago
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| add --phytozome to formats.gff.format() |
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over 10 years ago
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| + Add landscape.multilineplot() to plot one or more line plots in vertical stack + Adjust some standard paths in apps.base.set_home() |
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over 10 years ago
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| add shuffle to randomly inserted colors in graphics.base.AbstractLayout |
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over 10 years ago
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| embed branch length in projects.misc.birch() |
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over 10 years ago
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| remove augustus line |
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over 10 years ago
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| change default binary path in projects.tgbs.novo() |
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over 10 years ago
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| + Deprecate slow topological sort method and replace with genometools wrapper |
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over 10 years ago
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| + Add missing closing parens |
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over 10 years ago
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| + Allow processing specific feature type in formats.gff.format() + Extend formats.gff.extract() to accept either files with contigID/names or comma separated list |
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over 10 years ago
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| automatically select scoring params in formats.chain.last() |
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over 10 years ago
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| fix clr in assembly.ca.bisect() |
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over 10 years ago
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| add assembly.ca.bisect() |
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over 10 years ago
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| add formats.fasta.qual() |
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over 10 years ago
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