| Updated formats.gff.load() with refined parameter names. Changed URL quoting/unquoting behavior of the GFF3 attributes based on GFF3 spec |
|
More...
|
almost 12 years ago
|
| simplify tandem merging in algorithms.synteny.mcscan(); write query and subject block sizes in algorithms.synteny.simple(); update keyword --split to --splitobject in formats.fasta.gaps() |
|
More...
|
almost 12 years ago
|
| modify minor params in algorithms.fractionation.napus() |
|
More...
|
almost 12 years ago
|
| summarize quartets in algorithms.fractionation.napus() |
|
More...
|
almost 12 years ago
|
| add option --unmapped to write unmapped reads in apps.bowtie.align() |
|
More...
|
almost 12 years ago
|
| fix docstring for apps.bowtie |
|
More...
|
almost 12 years ago
|
| modify apps.base.ActionDispatcher to provide better help; add per module __main__ file to introspect on modules |
|
More...
|
almost 12 years ago
|
| Minor fix to blast.covfilter() when iterating thru query_subject pairs |
|
More...
|
almost 12 years ago
|
| add op.basename in formats.sam.get_prefix() |
|
More...
|
almost 12 years ago
|
| add option --top in formats.blast.top10() |
|
More...
|
almost 12 years ago
|
| add assembly.preprocess.contamination to check against Ecoli contamination |
|
More...
|
almost 12 years ago
|
| add option --firstN to apps.bowtie.align() |
|
More...
|
almost 12 years ago
|
| chmod after writing "run.sh" script |
|
More...
|
almost 12 years ago
|
| split FASTA automatically in assembly.ca.fasta() |
|
More...
|
almost 12 years ago
|
| fix -I in assembly.preprocess.alignextend() |
|
More...
|
almost 12 years ago
|
| modify fasta.filter() --less to be < instead of <= |
|
More...
|
almost 12 years ago
|
| add assembly.preprocess.alignextend(); handle --depth 1 as special case in assembly.ca.shred() |
|
More...
|
almost 12 years ago
|
| Merge branch 'master' of github.com:tanghaibao/jcvi |
|
More...
|
almost 12 years ago
|
| Updated formats.blast.covfilter() to allow iterating through and calculating covid for each query/subject pair; use the `--iterby` parameter. Fixed assembly.preprocess.trim() to report more informative AssertionError when Trimmomatic.jar file is missing |
|
More...
|
almost 12 years ago
|
| check clean FASTA in apps.vecscreen(); add option --tidy in assembly.ca.fasta() |
|
More...
|
almost 12 years ago
|
| Merge branch 'master' of github.com:tanghaibao/jcvi |
|
More...
|
almost 12 years ago
|
| Updated `add_attribute` option in formats.gff.format() to check if ID attribute exists or not. Fixed variable scope related issue in formats.blast.covfilter() |
|
More...
|
almost 12 years ago
|
| sort input files in assembly.automaton |
|
More...
|
almost 12 years ago
|
| clean up FASTA before convert FASTA to frg |
|
More...
|
almost 12 years ago
|
| allow formats.sam.consensus to generate FASTQ output |
|
More...
|
almost 12 years ago
|
| 1000th commit! add apps.bowtie() and simplify apps.bwa() |
|
More...
|
almost 12 years ago
|
| add options to SOAP assemblers; automate SOAP in assembly.automaton.soap() |
|
More...
|
almost 12 years ago
|
| export single reads in automaton.correct() |
|
More...
|
almost 12 years ago
|
| add assembly.automaton for automated assembly-related pipelines |
|
More...
|
about 12 years ago
|
| Merge branch 'master' of github.com:tanghaibao/jcvi |
|
More...
|
about 12 years ago
|
