| enforce --nogaps when --component is on in formats.agp.bed() |
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almost 13 years ago
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| add formats.gff.gapsplit() to spilt alignment GFF3 files (generated by GMAP) based on CIGAR encoding. Also added 'skipEmpty' parameter to GffLine.update_attributes() to allow skipping of empty tags in the attribute column |
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almost 13 years ago
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| fix invokation of run_formatdb() in apps.blastplus to check database stamps; allow writing to stdout when -o is not specified |
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almost 13 years ago
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| add formats.genbank.tofasta() |
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almost 13 years ago
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| make option --list to report non-mapped ids in formats.blast.covfilter() |
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almost 13 years ago
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| fix options in graphics.whisker |
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almost 13 years ago
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| add option --additional in algorithms.synteny.simple() |
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almost 13 years ago
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| add algorithms.synteny.simple to provide one-line description for blocks |
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almost 13 years ago
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| add graphics.whisker to generate boxplots for two-column data |
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almost 13 years ago
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| add algorithms.synteny.BoundaryFile class |
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almost 13 years ago
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| add singleton label in assembly.patch.paste() |
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almost 13 years ago
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| assign labels to paste flanks that failed to be incorporated |
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almost 13 years ago
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| add assembly.patch.paste() to paste in sequence components |
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almost 13 years ago
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| add option --union in formats.blast.covfilter() |
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almost 13 years ago
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| add utils.counter.Counter.report() |
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almost 13 years ago
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| add apps.ks.report() stats formatting |
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almost 13 years ago
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| provide better formatted statistics in apps.ks.report() |
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almost 13 years ago
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| change default style of apps.ks.multireport() and report() histogram |
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almost 13 years ago
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| add formats.blast.condense() |
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almost 13 years ago
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| deprecate formats.gff.script() and formats.fastq.pair() |
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almost 13 years ago
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| add formats.bed.flanking() |
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almost 13 years ago
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| add option --nofit in apps.ks.multireport() |
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almost 13 years ago
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| add assembly.ca.astat() |
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almost 13 years ago
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| add option --prefix in apps.cdhit.ids() |
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almost 13 years ago
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| add panel labels to graphics.paper.cotton() |
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almost 13 years ago
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| add graphics.glyph.RoundRect |
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almost 13 years ago
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| add depth distribution plot in graphics.paper.cotton() |
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almost 13 years ago
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| allow color spec in parsing simple anchors and blocks file |
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almost 13 years ago
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| fix function names in formats.genbank. (minor) |
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almost 13 years ago
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| add formats.genbank |
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almost 13 years ago
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