| add graphics.paper.litchi() |
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over 11 years ago
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| add option sep to utils.counter.Counter.report() |
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over 11 years ago
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| update Assembly.py of PBJELLY in assembly.pbjelly |
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over 11 years ago
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| update assembly.pbjelly command call |
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over 11 years ago
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| update ggplot2 code in graphics.histogram |
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over 11 years ago
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| Merge branch 'master' of github.com:tanghaibao/jcvi |
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almost 12 years ago
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| change --cpus in assembly.automaton.tophat(); change assembly.preprocess.count() to print to stderr |
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almost 12 years ago
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| add two tophat options in assembly.automaton.tophat() |
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almost 12 years ago
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| add assembly.automaton.tophat |
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almost 12 years ago
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| report full number in assembly.preprocess.count() and add option --human |
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almost 12 years ago
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| quote identifier in formats.gff.GffLine.accn |
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almost 12 years ago
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| add output option in assembly.preprocess.count() |
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almost 12 years ago
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| Selectively perform urlquoting of GFF3 attribute values based on attribute name; if 9th column of GFF3 file is missing, instantiate an empty attribute string and invent IDs wherever necessary |
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almost 12 years ago
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| Updated formats.gff.format() to allow multiple attributes/DBxref files to be processed at the same time; parallelized formats.gff.dedup_pile() to work on multiple piles at the same time (some issues with gffutils raising a DatabaseError when multiple processes are trying to read sqlite DB at the same time, observed when >=8 processes are running) |
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almost 12 years ago
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| show error messages when savefig fails |
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almost 12 years ago
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| Added in an option `--dedup` to formats.gff.uniq() to deduplicate the gene structures in a pile (after they have been filtered by score/span) |
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almost 12 years ago
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| Updated formats.gff.GffLine.set_attr() to not append values to attributes by default; added new option --dbxref to a `Dbxref` attribute |
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almost 12 years ago
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| Merge branch 'master' of github.com:tanghaibao/jcvi |
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almost 12 years ago
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| add --tags in graphics.histogram when plotting multiple data files |
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almost 12 years ago
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| Allow user to specify a notification message in apps.base.waitpid() |
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almost 12 years ago
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| add compara.fractionation.merge() |
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almost 12 years ago
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| switch arg positions for compara.catalog.ortholog() |
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almost 12 years ago
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| add 'extend' in utils.range.range_intersect(); add subject mode in formats.blast.best(); output new blastfile with --writeblast in formats.blast.cscore() |
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almost 12 years ago
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| add variation.delly |
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almost 12 years ago
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| add --mode to formats.bed.bins() |
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almost 12 years ago
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| reinstate algorithms.__main__ |
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almost 12 years ago
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| add default string formatter in apps.base |
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almost 12 years ago
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| add variation.snp.freq() |
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almost 12 years ago
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| add freebayes to formats.sam.bcf() |
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almost 12 years ago
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| add apps.bwa.mem() and set it as default mode for apps.bwa.align() |
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almost 12 years ago
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