| fix path in apps.softlink.link() |
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over 10 years ago
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| add assembly.meraculous |
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over 10 years ago
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| - Remove `dedup` option in formats.gff.uniq() (will be re-implemented later) |
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over 10 years ago
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| check read size before splitting in formats.fastq.splitread() |
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over 10 years ago
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| fix ALLPATHS-LG run script |
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over 10 years ago
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| skip empty groups |
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over 10 years ago
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| allow mixed fastq encodings in assembly.allpaths.prepare() |
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over 10 years ago
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| + Update pasa.consolidate() to cluster loci either based on coords or name + Update grid.array() to write individual log file and error file + Restrict gff.format() chaindup to features sharing same ID and located on same seqid |
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over 10 years ago
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| catch errors when variable label sizing fails |
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over 10 years ago
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| + Removed requirement to specify genome and transcripts fasta file for annotation.pasa.compare() (assumes that both fasta files are present) + Added param `--annots_gff3` to specify reference annotation gff3 + Adjust gff ID prefix separator to "|" in annotation.pasa.consolidate() |
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over 10 years ago
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| add --span in formats.gff.bed() |
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over 10 years ago
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| add --largest to assembly.ca.graph() |
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over 10 years ago
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| add assembly.ca.graph() |
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over 10 years ago
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| update README |
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over 10 years ago
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| add --removeoutliers in assembly.allmaps.path() |
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over 10 years ago
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| Merge branch 'master' of github.com:tanghaibao/jcvi |
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over 10 years ago
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| add --compress to assembly.allmaps |
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over 10 years ago
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| add apps.restriction.digest() |
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over 10 years ago
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| + Add option to specify FL accs list in pasa.assemble() |
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over 10 years ago
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| + Symlink genome/transcript fasta to PASA rundir in pasa.assemble() + Add `max number of transcripts per isoform` metric to stats.genestats() |
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over 10 years ago
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| replace data_files with package_data in setup.py |
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over 10 years ago
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| simplify calls to apps.base.dmain() |
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over 10 years ago
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| add --nodesc in formats.fasta.format() |
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over 10 years ago
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| simplify graphics.mummerplot() |
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over 10 years ago
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| + Minor change to formats.gff.match_subfeats() logic |
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over 10 years ago
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| + Move match_subfeats() from annotatIon.pasa() to format.gff() |
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over 10 years ago
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| + Precompute len(mrna) to speed up length filtering of transcripts + Address edge case affecting collapse of identical transcripts |
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over 10 years ago
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| + Fix mrna ID flattening in annotation.pasa.consolidate() + Fix usage of opts.gff3 parameter in formats.gff.format() + Add `--gg_cpu` option to assembly.trinity.prepare() to allow explicit setting of GG-Trinity CPU for each bin, independent of the CPU setting for the upstream steps (GSNAP, BAM coordinate sorting) |
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over 10 years ago
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| + annotation.pasa.consolidate() now prints gff3 to stdout + summary table (presence, absence) is printed to stderr + using `--slop` picks longest in every group of similar mrnas |
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over 10 years ago
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| add more readtypes in apps.bwa.align() |
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over 10 years ago
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