| add --coords to algorithms.synteny.simple() |
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almost 12 years ago
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| put N as postional argument instead option in formats.base.split() |
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almost 12 years ago
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| add mode "optimal" in formats.base.split(), remove option --cycle |
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almost 12 years ago
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| allow N=1 in annotation.maker.parallel() |
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almost 12 years ago
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| automatically re-generate failed sequence batch in annotation.maker() |
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almost 12 years ago
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| add annotation.maker.validate() to check for failures |
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almost 12 years ago
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| move apps.base.blast() to apps.align.blast() |
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almost 12 years ago
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| use central options for alignment --pctid, --pctcov, --evalue, etc. |
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almost 12 years ago
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| allow --pctid to be float |
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almost 12 years ago
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| Improve patching heuristics in assembly.sspace.embed() |
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almost 12 years ago
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| add --minspan to formats.bed.fix() |
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almost 12 years ago
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| use loghistogram in formats.agp.gaps(); add --swap to formats.blast.bed() |
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almost 12 years ago
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| pass all alignment cutoffs (pctid, overlap, overhang) to assembly.goldenpath.Overlap |
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almost 12 years ago
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| add WriteJobs in apps.grid for "multiple producers - one consumer" parallelization |
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almost 12 years ago
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| CHANGE MOptionParser back to OptionParser (override) |
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almost 12 years ago
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| BIG CHANGE. Wrap all OptionParser into apps.base.MOptionParser. |
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almost 12 years ago
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| handle case "b ~ a" in assembly.goldenpath.anneal() |
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almost 12 years ago
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| Use set() instead of list in annotation.reformat.reindex() and publocus() to count duplicate isoform only once. Add option to utils.sybase.query() to explicitly allow specification of an outfut field separator. Add check to apps.grid.run() to count number of args and display help message if no args specified |
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almost 12 years ago
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| Updated annotation.reformat.atg_name() to make use of RegExp to efficiently parse locus identifiers. Added two new options `reindex()` and `publocus()` to annnotation.reformat which work on lists of gene model identifiers. Updated utils.sybase.get_config() to properly get the name of the sybase server. Separated the connect() and the execute() to allow reuse of the db cursor. Added a new option `query()` which accepts queries with(out) placeholders; these placeholders are filled up with data coming from tab-delimited input file(s) |
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almost 12 years ago
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| write to dedup FASTA in assembly.goldenpath.dedup() |
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almost 12 years ago
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| add assembly.goldenpath.dedup() |
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almost 12 years ago
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| refactor formats.fasta.tidy() |
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almost 12 years ago
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| add more debug info in formats.fasta.gaps() |
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almost 12 years ago
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| add assembly.sspace.partition() |
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almost 12 years ago
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| fix formats.agp.tidy() |
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almost 12 years ago
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| allow annealing based on shred names in assembly.goldenpath.anneal() |
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almost 12 years ago
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| add conversion between CLR and AGPLine |
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almost 12 years ago
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| stringify tag=value in annotation.maker |
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almost 12 years ago
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| add --est in apps.cdhit.deduplicate() |
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almost 12 years ago
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| add --cleanfasta in assembly.pbjelly.patch() |
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almost 12 years ago
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