| Updated formats.bed.gff() to better handle missing fields in bed file. Added `--log` parameter to assembly.preprocess.trim(). Added `--add_attrib` parameter which takes a two-column tab delimiter file containing ID to look for in GFF file and attribute value to add (attribute name will be the name of the file) |
|
More...
|
about 12 years ago
|
| check file handle after checkexists in must_open() |
|
More...
|
about 12 years ago
|
| refactor annotation.evm; move apps.base.write_file() to formats.base.write_file() |
|
More...
|
about 12 years ago
|
| add option --fatten to graphics.landscape.composite() |
|
More...
|
about 12 years ago
|
| default to fasta format in formats.base.split() |
|
More...
|
about 12 years ago
|
| add option --fasta to assembly.kmer.jellyfish() |
|
More...
|
about 12 years ago
|
| add formats.bed.fix() to fix wrongly-formatted bed files |
|
More...
|
about 12 years ago
|
| add graphics.landscape.composite() to consolidate various types of plots along a chromosome |
|
More...
|
about 12 years ago
|
| add assembly.scaffold to scaffold with long reads |
|
More...
|
about 12 years ago
|
| add annotation.train.genemark() |
|
More...
|
about 12 years ago
|
| minor fix in annotation.train.pasa() |
|
More...
|
about 12 years ago
|
| clean up apps.blastplus to look like apps.last, remove grid option |
|
More...
|
about 12 years ago
|
| filter to get complete models following annotation.train.pasa() |
|
More...
|
about 12 years ago
|
| add option --scov in formats.blast.covfilter() |
|
More...
|
about 12 years ago
|
| add utils.taxonomy.newick() |
|
More...
|
about 12 years ago
|
| fix previous commit |
|
More...
|
about 12 years ago
|
| disable gff type checking when input is stdin |
|
More...
|
about 12 years ago
|
| fix minor issue with chr breaks in assembly.geneticmap.LD() |
|
More...
|
about 12 years ago
|
| add LD plot option to assembly.geneticmap.LD() |
|
More...
|
about 12 years ago
|
| add maximum coverage allowed in parsing the kmer distribution |
|
More...
|
about 12 years ago
|
| change default blast to get only best hit for assembly.postprocess.screen() |
|
More...
|
about 12 years ago
|
| move --pctid flag into blast in assembly.postprocess.screen() |
|
More...
|
about 12 years ago
|
| Updated formats.fastq.some() to now use a dict of ids to check against when pulling sequences from the input fastqfile(s) |
|
More...
|
about 12 years ago
|
| add option --leaffont in graphics.tree |
|
More...
|
about 12 years ago
|
| remove redundant code in formats.btab.gff() |
|
More...
|
about 12 years ago
|
| add default type "protein_match" in formats.btab.gff() |
|
More...
|
about 12 years ago
|
| Updated formats.fasta.identical() to now print out sequences unique to all input files |
|
More...
|
about 12 years ago
|
| simplify code in formats.btab.gff() |
|
More...
|
about 12 years ago
|
| add annotation.train() to train matrix for SNAP and AUGUSTUS |
|
More...
|
about 12 years ago
|
| add --nosim in allpaths fastq dump |
|
More...
|
about 12 years ago
|
