| add algorithms.fractionation.gffselect() |
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over 12 years ago
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| add options --synonymous and --fourfold to apps.phylo.build() to subset sequence alignment |
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over 12 years ago
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| add algorithms.fractionation.validate() to confirm the gene loss has no CDS overlaps |
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over 12 years ago
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| Augment annotation.reformat.annotate() to now allow assignment of identifiers based on `overlap` length in addition to the global sequence `alignment` score |
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over 12 years ago
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| add option --upper to formats.fasta.format() |
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over 12 years ago
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| allow --scaffold option in assembly.soap.prepare(); move cscore filtering before tandem removal in apps.blastfilter(); allow algorithms.synteny.liftover() to lift anchor pairs outside the initial bounding box. |
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over 12 years ago
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| add option --newfasta to assembly.postprocess.screen() |
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over 12 years ago
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| rename assembly.finish to assembly.postprocess and add function screen() |
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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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| Added functionality to formats.gff.format() to allow modification of GFF source field based on a two-column mapping file. Updated annotation.ahrd.fix() to retain and transfer any IPR and GO terms from the original AHRD to the fixed AHRD csv file |
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over 12 years ago
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| add option --tag in formats.gff.extract() |
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over 12 years ago
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| Minor update to formats.gff.format() which avoids introducting an empty `Name` attribute into the 9th column of the GFF file when trying to add a note field. Make `pvalue` field of BtabLine in formats.btab optional |
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over 12 years ago
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| adjust filesplitter zero-padding |
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over 12 years ago
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| make gaps.bed optional in annotation.reformat.rename() |
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over 12 years ago
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| Fix logic in the conditional statement that checks to see if an identifier from the `old.bed` file is being assigned to a gene model in the `new.bed` file which resides on a different reference sequence |
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over 12 years ago
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| Added annotation.reformat.annotate() to annotate new gene model set with identifiers from an old set; using pybedtools; pipeline relies on Needleman-Wunsch alignment scores to resolve ambiguous loci; will update pipeline to directly call apps.emboss.needle() once multiprocessing is implemented. Fixed module imports in assembly.deconvolute. Added new options to formats.bed.mergeBed() |
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over 12 years ago
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| minor modifications in the header fonts in graphics.histogram() |
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over 12 years ago
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| add algorithms.fractionation.gaps() |
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over 12 years ago
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| add algorithms.fractionation.status() and summary() |
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over 12 years ago
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| change algorithms.catalog.ortholog() pipeline - now perform quota first then liftover |
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over 12 years ago
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| handles no signal case in read_block() |
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over 12 years ago
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| typo in assembly.kmer.histogram() |
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over 12 years ago
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| simplify assembly.kmer.histogram() |
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over 12 years ago
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| make apps.bwa only output the best alignment (-n 1) |
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over 12 years ago
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| simplify formats.fastq.first() |
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over 12 years ago
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| add --evalue to apps.base.blast() |
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over 12 years ago
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| add apps.emboss to run EMBOSS applications |
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over 12 years ago
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| make apps.base py2.5 compatible |
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over 12 years ago
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| Update formats.gff.format() --unique option to track any duplicate `ID` which is a `Parent` of another feature and appropriately change the `Parent` field of that feature to reflect the new unique `ID`. Add new RegExp to fix TAIR10 headers |
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over 12 years ago
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| flip reads when output mate pair fastq in assembly.preprocess.correct() |
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over 12 years ago
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