| change set_sort_tmpdir() to set_tmpdir(); add set_tmpdir() to annotation.maker.parallel() |
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almost 12 years ago
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| add annotation.maker.merge() |
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almost 12 years ago
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| avoid double @ in assembly.deconvolute |
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almost 12 years ago
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| add Overlap.anneal() in assembly.goldenpath |
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almost 12 years ago
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| add assembly.goldenpath.anneal() |
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almost 12 years ago
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| add option --inplace for formats.agp.reindex() |
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almost 12 years ago
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| add option --shift in assembly.ca.shred() |
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almost 12 years ago
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| use fasta.format() in assembly.pbjelly to clean up |
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almost 12 years ago
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| recruite singletons in assembly.sspace |
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almost 12 years ago
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| update lines after delete in formats.agp.AGP |
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almost 12 years ago
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| simplify write_file(meta="run script") |
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almost 12 years ago
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| add BiGraph.add_node() and add_edge() |
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almost 12 years ago
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| add update subroutines to AGP record |
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almost 12 years ago
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| add assembly.sspace.anchor() [work incomplete] |
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almost 12 years ago
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| make formats.fasta.gaps() option --split conform to gapSplit |
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almost 12 years ago
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| allow assembly.deconvolute to deconvolute paired reads through --paired |
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almost 12 years ago
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| add formats.sam.coverage() |
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almost 12 years ago
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| improve performance when writing qual file |
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almost 12 years ago
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| add annotation.maker.parallel() to parallelize maker on the grid |
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almost 12 years ago
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| massively simplifiy apps.grid; add apps.grid.array to run array job |
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almost 12 years ago
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| Modified formats.base.flatten() to allow zipping of table elements before flattening |
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almost 12 years ago
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| Added `keysep` option to formats.base.join() to specify whether the `key` column in the pivot file contains delimiter-separated elements or not; if True, matching rows are zipped together to create one row in the output file |
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almost 12 years ago
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| add option --augustus to formats.gff.fromgtf() |
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almost 12 years ago
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| Change default behavior of formats.base.group() to group all the elements in the input file, not based on any particular column. |
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almost 12 years ago
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| add assembly.pbjelly to pipeline the PBJelly data prep and parallelize PBJelly assembly |
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almost 12 years ago
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| add formats.fastq.fasta() |
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almost 12 years ago
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| propagate --rclip through a few functions involved in bambus scaffolding |
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about 12 years ago
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| Use a set() instead of a list in formats.base.group() to ignore any duplicate values when grouping |
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about 12 years ago
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| Added new ACTION `group` to formats.base to allow grouping of elements in a multi-column table based on a key(groupby) column. Added new class to utils.cbook to allow Autovivification, similar to Perl. Minor changes to formats.gff.GffLine() for better URL quoting |
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about 12 years ago
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| add apps.ks.subset() to extract part of pre-calc Ks values; allow optional pepfile input in apps.ks.prepare() |
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about 12 years ago
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