| add assembly.patch.mapbreaks() and assembly.patch.refine() |
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about 13 years ago
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| add assembly.opticalmap.chimera() to identify breakpoints according to OM |
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about 13 years ago
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| add assembly.opticalmap.fasta() to build pseudomolecules based on optical map |
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about 13 years ago
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| typo in assembly.soap.prepare() |
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about 13 years ago
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| add formats.fasta.clean() |
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about 13 years ago
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| add assembly.patch.certificate() |
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about 13 years ago
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| guess offset in assembly.preprocess.correct() |
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about 13 years ago
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| add assembly.patch for merging assemblies |
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about 13 years ago
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| add adapter seqs to assembly.preprocess |
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about 13 years ago
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| simplify assembly.ca.fastq() |
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about 13 years ago
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| modify formats.fastq.filter() to not use FastqGeneralIterator |
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about 13 years ago
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| add formats.fastq.filter() to get high qv reads |
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about 13 years ago
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| minor fix in get_binfiles in graphics.landscape |
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about 13 years ago
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| add --subtract in graphics.landscape() |
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about 13 years ago
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| use PLOIDY=2 as default when running ALLPATHS-LG |
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about 13 years ago
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| add clc_novo_assemble wrapper |
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about 13 years ago
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| add option --site to formats.fastq.deconvolute() |
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about 13 years ago
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| Removed jcvi.formats.fasta.togff() since similar functionality can be achieved by running jcvi.formats.sizes.agp() followed by jcvi.format.agp.bed() with the `--gff` command line option to generate GFF3 formatted output. |
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about 13 years ago
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| Added a @property to jcvi.formats.obo.GODag() which returns a list of OBO 'names' which can be used to cross-verify input SO terms. Added a routine to validate_terms() in jcvi.formats.bed. Augmented jcvi.formats.bed.agp() with gff specific options which also makes use of the SO term validation. |
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about 13 years ago
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| minor changes in graphics.landscape |
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about 13 years ago
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| Minor modification to ORFFinder class. Added jcvi.formats.fasta.togff() to generate a simple GFF3 file (for use with GBrowse) listing out each seq-region per sequence in the input FASTA file |
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about 13 years ago
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| add option --meres to graphics.landscape.heatmap() |
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over 13 years ago
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| Added `--longest` option to jcvi.formats.fasta.translate() to find the longest ORF for each input cDNA sequence. ORFFinder() code derived from a BioStar codegolf competition entry https://gist.github.com/933737 |
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over 13 years ago
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| fix bug in formats.bed.bins() |
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over 13 years ago
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| fix bug in utils.cbook.autoscale() |
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over 13 years ago
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| add utils.cbook.autoscale() and graphics.landscape.heatmap() |
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over 13 years ago
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| add graphics.landscape.stack() |
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over 13 years ago
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| add mummerplot wrapper |
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over 13 years ago
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| add richer report for GapCloser |
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over 13 years ago
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| minor fix in annotation.stats() |
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over 13 years ago
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